Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xds Working: n-9-23.cluster.ucsf.bkslab.org:/scratch/xiaobo/365617/xds-8058088.97 Result: /scratch/xiaobo/365617/xds-8058088.97 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xds Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xds mkdir: created directory `/scratch/xiaobo/365617' mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97' /scratch/xiaobo/365617/xds-8058088.97 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working' mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/protonate' Storing results in /scratch/xiaobo/365617/xds-8058088.97/finished Working in /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 /scratch/xiaobo/365617/xds-8058088.97/working/protonate /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Using inputs as protomers/tautomers. No processing done 450 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/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Bulk generating 3D conformations all protomers in /scratch/xiaobo/365617/xds-8058088.97/working/3D mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/365617/xds-8058088.97/working/protonate/xds-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 ZINC001271695049 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building' mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001271695049 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/1 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/1' -> `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]2COC[C@H](C1)N2C) `ZINC001271695049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695049 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2COC[C@H](C1)N2C NO_LONG_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', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 2, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5 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: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695049 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/finished' Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049/0.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695049 Building ZINC001271695442 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271695442 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/2 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/2' -> `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)C[C@@H](C1)O2) `ZINC001271695442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695442 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 12, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 6 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: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/3 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/3' -> `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)C[C@@H](C1)O2) `ZINC001271695442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695442 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 12, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 9 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: 29 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695442 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 Building ZINC001271695442 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271695442 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 2) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2) `ZINC001271695442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695442 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 12, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 6 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: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 3) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2) `ZINC001271695442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695442 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CN(C)C[C@@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 7, 5, 12, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 9 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: 29 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695442 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695442 Building ZINC001271695453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/4 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/5 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/6 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/6' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/7 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/7' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 Building ZINC001271695453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 4) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 5) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 6) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 7) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 Building ZINC001271695453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 4) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 5) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 6) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 7) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 Building ZINC001271695453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 4) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 5) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/5: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 6) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/6: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 30, 30, 30, 30, 30, 30, 45, 47, 47, 47, 47, 47, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 30, 30, 30, 30, 30, 30, 45, 45, 47, 47, 30, 30] 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: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 7) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271695453.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695453 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 49, 50, 50, 50, 50, 50, 33, 2, 2, 2, 2, 2, 2, 2, 2, 2, 35, 35, 35, 35, 35, 35, 49, 49, 50, 50, 35, 35] 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: 134 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695453 Building ZINC001271695980 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695980 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/8 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/9 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/10 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/10' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/11 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/11' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695980 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 Building ZINC001271695980 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695980 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 8) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 9) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 10) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 11) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695980 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 Building ZINC001271695980 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695980 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 8) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 9) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 10) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 11) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695980 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 Building ZINC001271695980 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271695980 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 8) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 9) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/9: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 10) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/10: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 4, 18, 18, 16, 18, 18, 18, 18, 37, 37, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 17, 18, 18, 18, 18, 18, 18, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 11) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/11: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2) `ZINC001271695980.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271695980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271695980 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(C1)CCN(CCN(C)C)C2 NO_LONG_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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 5, 19, 20, 18, 20, 20, 20, 20, 38, 38, 50, 50, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 19, 20, 20, 20, 20, 38, 38, 38, 38, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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/365617/xds-8058088.97/working/building/ZINC001271695980 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271695980 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271695980 Building ZINC001271696132 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696132 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/12 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/13 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/14 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/14' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/15 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/15' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696132 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 Building ZINC001271696132 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696132 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 12) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 13) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 14) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 15) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696132 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 Building ZINC001271696132 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696132 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 12) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 13) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 14) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 15) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696132 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 Building ZINC001271696132 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696132 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 12) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/12: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 13) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/13: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 14) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/14: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 22, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 37 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 15) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/15: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)C1) `ZINC001271696132.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696132 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 12, 19, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 25 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696132 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696132 Building ZINC001271696134 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696134 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/16 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/17 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/18 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/18' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/19 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/19' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696134 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 Building ZINC001271696134 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696134 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 16) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 17) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 18) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 19) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696134 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 Building ZINC001271696134 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696134 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 16) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 17) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 18) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 19) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696134 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 Building ZINC001271696134 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271696134 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 16) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 17) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 18) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 2, 19, 29, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 47 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 77 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 19) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/19: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)C1) `ZINC001271696134.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271696134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271696134 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC[C@@]2(CN(C)CCO2)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.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 10, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 2, 14, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271696134 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271696134 Building ZINC000194622787 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194622787 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/20 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194622787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194622787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622787 none C[C@@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 4] 12 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/21 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194622787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194622787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622787 none C[C@@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 11 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194622787 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 Building ZINC000194622787 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194622787 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 20) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194622787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194622787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622787 none C[C@@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 2, 9, 1, 1, 1, 4, 4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 1, 4, 4] 12 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 21) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194622787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194622787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622787 none C[C@@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 11 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194622787 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622787 Building ZINC000194622804 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194622804 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/22 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194622804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194622804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622804 none C[C@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 12 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 26 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/23 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194622804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194622804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622804 none C[C@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 4] 10 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194622804 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 Building ZINC000194622804 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194622804 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 22) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194622804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194622804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622804 none C[C@H]1C(=O)N(C)CCN1C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 2, 8, 1, 1, 1, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 3, 3] 12 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 26 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 23) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194622804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194622804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000194622804 none C[C@H]1C(=O)N(C)CCN1C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 2, 7, 1, 1, 1, 4, 4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 4] 10 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194622804 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194622804 Building ZINC001271697552 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271697552 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/24 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/24' -> `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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/25 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/25' -> `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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/26 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/26' -> `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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/27 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/27' -> `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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697552 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 Building ZINC001271697552 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271697552 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 24) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 25) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 26) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 27) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697552 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 Building ZINC001271697552 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271697552 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 24) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 25) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 26) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 27) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697552 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 Building ZINC001271697552 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271697552 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 24) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 25) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 26) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/26: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 2, 2, 1, 1, 1, 1, 5, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 20 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: 31 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 27) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2OCCN(C)[C@H]2C1) `ZINC001271697552.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271697552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697552 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@@H]2OCCN(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', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11] 13 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: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697552 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697552 Building ZINC001271697844 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271697844 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/28 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271697844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697844 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 31, 18, 31, 18, 25, 48, 50, 50, 50, 50, 50, 31, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 48, 48, 50, 50, 31, 31, 31, 31] 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: 303 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/29 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/29' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271697844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697844 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 29, 19, 29, 19, 23, 48, 50, 50, 50, 50, 50, 29, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 48, 48, 50, 50, 29, 29, 29, 29] 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: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697844 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 Building ZINC001271697844 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271697844 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 28) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271697844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271697844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697844 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 31, 18, 31, 18, 25, 48, 50, 50, 50, 50, 50, 31, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 31, 31, 31, 31, 48, 48, 50, 50, 31, 31, 31, 31] 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: 303 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 29) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271697844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271697844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271697844 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 4, 29, 19, 29, 19, 23, 48, 50, 50, 50, 50, 50, 29, 24, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29, 48, 48, 50, 50, 29, 29, 29, 29] 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: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271697844 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271697844 Building ZINC001271694069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/30 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/31 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/32 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/32' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/33 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/33' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 Building ZINC001271694069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 30) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 31) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 32) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 33) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 Building ZINC001271694069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 30) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 31) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 32) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 33) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 Building ZINC001271694069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 30) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 31) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 32) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/32: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 26, 15, 15, 15, 15, 15, 15, 1, 1, 3, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 26, 26, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 33) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694069.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694069 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 25, 14, 14, 14, 14, 14, 14, 2, 1, 4, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 25, 25, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694069 Building ZINC001271694147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/34 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/34' -> `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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/35 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/35' -> `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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/36 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/36' -> `2.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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/37 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/37' -> `3.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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 Building ZINC001271694147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 34) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 35) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 36) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 37) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 Building ZINC001271694147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 34) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 35) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 36) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 37) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 Building ZINC001271694147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 34) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 35) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 36) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 9, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 38, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19, 19, 19, 19, 19, 19, 19, 38, 38, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 37) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/37: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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]2[C@@H]1CCN2CCN(C)C) `ZINC001271694147.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694147 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2[C@@H]1CCN2CCN(C)C NO_LONG_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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 6, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 41, 43, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17, 17, 17, 17, 17, 17, 17, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694147 Building ZINC001271694171 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694171 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/38 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C) `ZINC001271694171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694171 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 38, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 33, 33, 38, 38, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/39 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C) `ZINC001271694171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694171 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 36, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 36, 36, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694171 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 Building ZINC001271694171 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694171 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 38) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/38: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C) `ZINC001271694171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694171 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 4, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 33, 38, 48, 48, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 33, 33, 38, 38, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 39) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C) `ZINC001271694171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694171 none CC(C)C[C@]([O-])([SiH3])C(=O)N1C[C@H]2CC[C@@H](C1)N2CCN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 36, 42, 50, 50, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 36, 36, 42, 42, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 200 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694171 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694171 Building ZINC001271694285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/40 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/41 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/42 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/42' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/43 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/43' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 Building ZINC001271694285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 40) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 41) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 42) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 43) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 Building ZINC001271694285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 40) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 41) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 42) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 43) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 Building ZINC001271694285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 40) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 41) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 42) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/42: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 32, 37, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 32, 32, 37, 37, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 43) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/43: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)C)C1) `ZINC001271694285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694285 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CCN2CCN(C)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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 21, 21, 21, 21, 21, 21, 34, 39, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 21, 21, 21, 21, 34, 34, 39, 39, 50, 50, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694285 Building ZINC001271694362 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694362 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/44 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])CC(C)C) `ZINC001271694362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271694362 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 16, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/45 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])CC(C)C) `ZINC001271694362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271694362 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 16, 16, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694362 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 Building ZINC001271694362 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694362 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 44) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])CC(C)C) `ZINC001271694362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271694362 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 34, 16, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 16, 16, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 45) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])CC(C)C) `ZINC001271694362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271694362 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 45, 45, 16, 16, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694362 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694362 Building ZINC001271694376 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694376 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/46 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)C2)C1) `ZINC001271694376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694376 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 9, 21, 21, 21, 21, 21, 36, 36, 36, 46, 46, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 46, 46, 46, 46, 46, 46, 46, 21, 21, 21, 21] 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: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/47 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)C2)C1) `ZINC001271694376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694376 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 27, 27, 27, 43, 43, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 27, 43, 43, 43, 43, 43, 43, 43, 12, 12, 12, 12] 47 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: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694376 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 Building ZINC001271694376 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694376 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 46) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)C2)C1) `ZINC001271694376.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694376 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 9, 21, 21, 21, 21, 21, 36, 36, 36, 46, 46, 21, 21, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 21, 21, 36, 46, 46, 46, 46, 46, 46, 46, 21, 21, 21, 21] 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: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 47) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)C2)C1) `ZINC001271694376.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694376 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(C(=O)NC(C)C)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 5, 12, 12, 12, 12, 12, 27, 27, 27, 43, 43, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 27, 43, 43, 43, 43, 43, 43, 43, 12, 12, 12, 12] 47 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: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694376 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694376 Building ZINC001271694380 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694380 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/48 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694380 none COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 33, 13, 10, 16, 10, 16, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 49, 49, 33, 33, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/49 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/49' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694380 none COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 13, 9, 16, 9, 16, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 49, 49, 28, 28, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694380 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 Building ZINC001271694380 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694380 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 48) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694380 none COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 33, 13, 10, 16, 10, 16, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 49, 49, 33, 33, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 49) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2) `ZINC001271694380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271694380 none COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])CC(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 28, 13, 9, 16, 9, 16, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 49, 49, 28, 28, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694380 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694380 Building ZINC001271694684 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694684 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/50 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)C2)C1) `ZINC001271694684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694684 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)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', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 25, 15, 25, 15, 19, 33, 38, 50, 50, 25, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 33, 33, 38, 38, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 302 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/51 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)C2)C1) `ZINC001271694684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694684 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)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', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 27, 15, 27, 15, 21, 32, 36, 50, 50, 27, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 32, 32, 36, 36, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 303 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694684 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 Building ZINC001271694684 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271694684 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 50) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)C2)C1) `ZINC001271694684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694684 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)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', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 25, 15, 25, 15, 19, 33, 38, 50, 50, 25, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 25, 25, 25, 25, 33, 33, 38, 38, 50, 50, 50, 50, 50, 50, 25, 25, 25, 25] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 302 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 51) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)C2)C1) `ZINC001271694684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694684 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC2(CN(CCN(C)C)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', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 3, 3, 27, 15, 27, 15, 21, 32, 36, 50, 50, 27, 22, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 32, 32, 36, 36, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 303 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694684 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694684 Building ZINC001271694818 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694818 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/52 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/52' -> `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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/53 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/53' -> `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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/54 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/54' -> `2.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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/55 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/55' -> `3.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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694818 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 Building ZINC001271694818 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694818 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 52) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 53) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 54) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 55) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694818 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 Building ZINC001271694818 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694818 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 52) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 53) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 54) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 55) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694818 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 Building ZINC001271694818 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271694818 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 52) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 53) grep: /scratch/xiaobo/365617/xds-8058088.97/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)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 54) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/54: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 7, 10, 16, 16, 16, 16, 16, 16, 16, 34, 36, 50, 50, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 34, 34, 36, 36, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 55) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/55: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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(CCN(C)C)C[C@H]21) `ZINC001271694818.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271694818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271694818 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CC[C@H]2CN(CCN(C)C)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.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 10, 5, 5, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 1, 5, 8, 14, 14, 14, 14, 14, 14, 14, 32, 38, 50, 50, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 14, 14, 14, 14, 32, 32, 38, 38, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271694818 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271694818 Building ZINC000487484424 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487484424 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/56 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000487484424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487484424 none COC(=O)[C@]1(C)CCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 39, 16, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 39, 39, 39, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/57 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@]1(C)CCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000487484424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487484424 none COC(=O)[C@]1(C)CCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 11, 38, 11, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487484424 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 Building ZINC000487484424 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487484424 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 56) grep: /scratch/xiaobo/365617/xds-8058088.97/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@]1(C)CCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000487484424.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487484424 none COC(=O)[C@]1(C)CCCN1C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 39, 16, 16, 16, 16, 16, 6, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 39, 39, 39, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 57) grep: /scratch/xiaobo/365617/xds-8058088.97/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@]1(C)CCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000487484424.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487484424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487484424 none COC(=O)[C@]1(C)CCCN1C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 11, 38, 11, 11, 11, 11, 11, 6, 1, 7, 1, 1, 1, 7, 7, 7, 7, 7, 38, 38, 38, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 105 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487484424 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487484424 Building ZINC001271718610 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271718610 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/58 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271718610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271718610 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 36, 49, 36, 22, 36, 22, 22, 22, 22, 22, 5, 1, 9, 1, 1, 1, 7, 7, 22, 49, 49, 49, 49, 49, 49, 49, 36, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/59 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271718610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271718610 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 37, 49, 37, 20, 37, 20, 20, 20, 20, 20, 5, 1, 9, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 49, 49, 49, 37, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718610 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 Building ZINC001271718610 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271718610 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 58) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271718610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271718610 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 36, 49, 36, 22, 36, 22, 22, 22, 22, 22, 5, 1, 9, 1, 1, 1, 7, 7, 22, 49, 49, 49, 49, 49, 49, 49, 36, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 59) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271718610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271718610 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 37, 49, 37, 20, 37, 20, 20, 20, 20, 20, 5, 1, 9, 1, 1, 1, 6, 6, 20, 49, 49, 49, 49, 49, 49, 49, 37, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718610 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718610 Building ZINC001271718144 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718144 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/60 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/61 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/62 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/62' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/63 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/63' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718144 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 Building ZINC001271718144 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718144 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 60) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 61) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 62) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 63) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718144 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 Building ZINC001271718144 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718144 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 60) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 61) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 62) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 63) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718144 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 Building ZINC001271718144 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718144 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 60) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 61) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 23, 23, 23, 23, 23, 23, 4, 1, 12, 1, 1, 1, 3, 3, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23, 23, 23] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 62) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/62: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 63) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/63: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271718144.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271718144 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 20, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 20, 20, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718144 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718144 Building ZINC001271718178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/64 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/65 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/66 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/66' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/67 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/67' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 Building ZINC001271718178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 64) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 65) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 66) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 67) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 Building ZINC001271718178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 64) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 65) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 66) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 67) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 Building ZINC001271718178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271718178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 64) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 65) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 23, 23, 23, 23, 23, 23, 23, 12, 1, 10, 1, 1, 1, 3, 3, 23, 23, 23, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 23, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 66) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/66: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 67) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/67: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271718178.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271718178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271718178 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 31, 45, 31, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 5, 5, 17, 17, 17, 45, 45, 45, 45, 45, 45, 31, 31, 31, 31, 17, 17, 17, 17, 17, 17, 5, 5, 5, 5, 5, 17, 17] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271718178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271718178 Building ZINC001271719100 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719100 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/68 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271719100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719100 none CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 50, 31, 16, 31, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 31, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/69 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271719100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719100 none CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 46, 28, 16, 28, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 5, 5, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 28, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719100 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 Building ZINC001271719100 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719100 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 68) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/68: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271719100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719100 none CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 50, 31, 16, 31, 16, 16, 16, 16, 16, 16, 9, 1, 9, 1, 1, 1, 5, 5, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 31, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 69) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/69: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1) `ZINC001271719100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719100 none CC(C)NC(=O)N1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C3CC3)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 28, 46, 28, 16, 28, 16, 16, 16, 16, 16, 16, 10, 1, 10, 1, 1, 1, 5, 5, 16, 16, 16, 46, 46, 46, 46, 46, 46, 46, 28, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719100 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719100 Building ZINC001271719275 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719275 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/70 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719275 none CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 44, 27, 9, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 9, 9, 44, 44, 44, 44, 44, 44, 44, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/71 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719275 none CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 25, 10, 25, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 41, 41, 41, 41, 41, 41, 41, 25, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719275 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 Building ZINC001271719275 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719275 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 70) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/70: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719275 none CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 44, 27, 9, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 9, 9, 44, 44, 44, 44, 44, 44, 44, 27, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 71) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/71: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719275 none CC(C)NC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 41, 25, 10, 25, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 6, 6, 41, 41, 41, 41, 41, 41, 41, 25, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719275 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719275 Building ZINC001271719303 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719303 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/72 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719303 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 10, 36, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 4, 4, 10, 50, 50, 50, 50, 50, 50, 50, 36, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/73 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719303 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 9, 50, 50, 50, 50, 50, 50, 50, 37, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719303 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 Building ZINC001271719303 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719303 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 72) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/72: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719303.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719303 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 10, 36, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 1, 4, 4, 10, 50, 50, 50, 50, 50, 50, 50, 36, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 73) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/73: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719303.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271719303 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 9, 37, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 4, 1, 1, 1, 6, 6, 9, 50, 50, 50, 50, 50, 50, 50, 37, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 6, 9, 9] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719303 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719303 Building ZINC001271719339 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719339 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/74 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/75 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/76 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/76' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/77 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/77' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719339 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 Building ZINC001271719339 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719339 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 74) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 75) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 76) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 77) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719339 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 Building ZINC001271719339 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719339 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 74) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 75) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 76) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 77) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719339 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 Building ZINC001271719339 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719339 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 74) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 75) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 34, 48, 34, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 1, 10, 1, 1, 1, 4, 4, 17, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 17, 17, 17, 17, 17, 17, 4, 4, 4, 4, 4, 17, 17] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 76) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/76: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 77) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719339.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719339 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 34, 15, 15, 15, 15, 15, 15, 15, 15, 15, 7, 1, 10, 1, 1, 1, 2, 2, 15, 50, 50, 50, 50, 50, 50, 35, 35, 34, 34, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 2, 15, 15] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 199 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719339 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719339 Building ZINC001271719342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/78 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/79 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/80 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/80' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/81 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/81' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 Building ZINC001271719342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 78) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 79) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 80) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 81) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 Building ZINC001271719342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 78) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 79) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 80) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 81) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 Building ZINC001271719342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 78) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 79) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 20, 20, 20, 20, 20, 28, 28, 50, 50, 50, 50, 19, 1, 1, 1, 4, 4, 20, 20, 20, 20, 20, 20, 28, 28, 28, 28, 50, 50, 50, 20, 20, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 80) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/80: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 81) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/81: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719342 none O=C(N1CC2(CCN2CCn2ccnc2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 15, 15, 15, 15, 15, 22, 24, 50, 50, 50, 50, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 15, 15, 22, 22, 24, 24, 50, 50, 50, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719342 Building ZINC001271719358 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719358 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/82 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719358 none O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 12, 15, 12, 14, 22, 26, 50, 50, 50, 50, 15, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 22, 22, 26, 26, 50, 50, 50, 15, 15, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/83 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719358 none O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 11, 20, 11, 16, 20, 24, 50, 50, 50, 50, 20, 16, 1, 1, 1, 3, 3, 20, 20, 20, 20, 20, 20, 24, 24, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719358 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 Building ZINC001271719358 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719358 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 82) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719358 none O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 15, 12, 15, 12, 14, 22, 26, 50, 50, 50, 50, 15, 14, 1, 1, 1, 4, 4, 15, 15, 15, 15, 22, 22, 26, 26, 50, 50, 50, 15, 15, 15, 15, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 83) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271719358 none O=C(N1CC2(CN(CCn3ccnc3)C2)C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 8, 1, 1, 8, 1, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 20, 11, 20, 11, 16, 20, 24, 50, 50, 50, 50, 20, 16, 1, 1, 1, 3, 3, 20, 20, 20, 20, 20, 20, 24, 24, 50, 50, 50, 20, 20, 20, 20, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719358 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719358 Building ZINC001271719612 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719612 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/84 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC12CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719612 none CC(C)NC(=O)N1CCC12CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 28, 44, 28, 20, 28, 20, 20, 20, 20, 20, 5, 1, 5, 1, 1, 1, 6, 6, 20, 44, 44, 44, 44, 44, 44, 44, 28, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/85 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/85' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC12CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719612 none CC(C)NC(=O)N1CCC12CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 30, 49, 30, 19, 30, 19, 19, 19, 19, 19, 5, 1, 5, 1, 1, 1, 6, 6, 19, 49, 49, 49, 49, 49, 49, 49, 30, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719612 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 Building ZINC001271719612 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719612 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 84) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)NC(=O)N1CCC12CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271719612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719612 none CC(C)NC(=O)N1CCC12CN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 28, 44, 28, 20, 28, 20, 20, 20, 20, 20, 5, 1, 5, 1, 1, 1, 6, 6, 20, 44, 44, 44, 44, 44, 44, 44, 28, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 85) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)NC(=O)N1CCC12CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271719612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719612 none CC(C)NC(=O)N1CCC12CN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens 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, 30, 49, 30, 19, 30, 19, 19, 19, 19, 19, 5, 1, 5, 1, 1, 1, 6, 6, 19, 49, 49, 49, 49, 49, 49, 49, 30, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 19, 19] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719612 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719612 Building ZINC001271719680 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719680 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/86 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719680 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 45, 26, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 5, 5, 45, 45, 45, 45, 45, 45, 30, 30, 26, 26, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/87 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719680 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 42, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 42, 42, 42, 42, 42, 42, 30, 30, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719680 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 Building ZINC001271719680 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719680 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 86) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719680.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719680 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 45, 26, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 5, 5, 45, 45, 45, 45, 45, 45, 30, 30, 26, 26, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 87) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719680.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719680 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 30, 42, 27, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 4, 4, 42, 42, 42, 42, 42, 42, 30, 30, 27, 27, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 166 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719680 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719680 Building ZINC001271719757 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719757 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/88 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719757 none O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10] 45 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/89 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719757 none O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 39, 39, 39, 39, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719757 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 Building ZINC001271719757 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719757 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 88) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719757 none O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 1, 1, 1, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10] 45 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 71 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 89) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719757 none O=C(N1C[C@@H]2COC[C@H](C1)N2C1CCCC1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 39, 39, 39, 39, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 39, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11, 11, 11, 11] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719757 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719757 Building ZINC001271719762 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719762 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/90 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/91 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/92 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/92' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/93 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/93' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719762 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 Building ZINC001271719762 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719762 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 90) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 91) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 92) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 93) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719762 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 Building ZINC001271719762 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719762 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 90) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 91) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 92) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 93) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719762 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 Building ZINC001271719762 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719762 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 90) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 91) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 25, 25, 25, 25, 25, 25, 25, 29, 46, 46, 46, 46, 25, 25, 23, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 46, 46, 46, 46, 46, 46, 46, 46, 46, 25, 25, 6, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 123 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 92) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/92: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 93) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/93: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1) `ZINC001271719762.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719762 none O=C(N1C[C@@H]2OCCN(C3CCCC3)[C@H]2C1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 12, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 24, 24, 24, 24, 24, 24, 24, 27, 46, 46, 46, 46, 24, 24, 22, 1, 1, 1, 7, 7, 24, 24, 24, 24, 24, 24, 46, 46, 46, 46, 46, 46, 46, 46, 46, 24, 24, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719762 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719762 Building ZINC001271719947 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719947 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/94 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271719947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271719947 none CC(C)NC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 37, 39, 37, 37, 37, 37, 37, 4, 1, 7, 1, 1, 1, 4, 4, 37, 37, 50, 50, 50, 50, 50, 50, 50, 39, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 37, 37, 37, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/95 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271719947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271719947 none CC(C)NC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 30, 36, 30, 30, 30, 30, 30, 4, 1, 8, 1, 1, 1, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 36, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 30, 30, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719947 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 Building ZINC001271719947 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719947 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 94) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/94: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271719947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271719947 none CC(C)NC(=O)N1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 37, 39, 37, 37, 37, 37, 37, 4, 1, 7, 1, 1, 1, 4, 4, 37, 37, 50, 50, 50, 50, 50, 50, 50, 39, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 37, 37, 37, 37] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 95) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/95: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1) `ZINC001271719947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271719947 none CC(C)NC(=O)N1CCC2(CN(C(=O)[C@]([O-])([SiH3])C3CC3)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 36, 30, 36, 30, 30, 30, 30, 30, 4, 1, 8, 1, 1, 1, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 36, 30, 30, 30, 30, 30, 30, 4, 4, 4, 4, 4, 30, 30, 30, 30] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719947 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719947 Building ZINC001271719957 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719957 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/96 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001271719957 none CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 47, 32, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 5, 5, 47, 47, 47, 47, 47, 47, 39, 39, 32, 32, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/97 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001271719957 none CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 48, 35, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 38, 38, 35, 35, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719957 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 Building ZINC001271719957 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719957 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 96) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719957.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001271719957 none CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 47, 32, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 5, 5, 47, 47, 47, 47, 47, 47, 39, 39, 32, 32, 20, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 97) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719957.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001271719957 none CN(C)CCNC1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 48, 35, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 38, 38, 35, 35, 25, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 182 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719957 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719957 Building ZINC001271719965 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719965 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/98 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719965 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 48, 30, 12, 30, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 48, 48, 30, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/99 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/99' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719965 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 46, 30, 12, 30, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 7, 7, 46, 46, 46, 46, 46, 46, 46, 30, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719965 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 Building ZINC001271719965 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719965 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 98) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/98: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719965 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 30, 48, 30, 12, 30, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 48, 48, 30, 12, 12, 12, 12, 12, 12, 6, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 99) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/99: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001271719965 none CC(C)NC(=O)N1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', '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, 8, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 30, 46, 30, 12, 30, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 7, 7, 46, 46, 46, 46, 46, 46, 46, 30, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719965 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719965 Building ZINC001271719982 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719982 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/100 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719982 none O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 19, 41, 41, 41, 41, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 13, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 13, 13, 13, 13, 9, 9, 9, 9, 9] 48 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/101 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/101' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@]([O-])([SiH3])C1CC1) `ZINC001271719982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719982 none O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 10, 10, 10, 10, 14, 28, 28, 28, 28, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 9, 9, 9, 9, 9] 38 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719982 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 Building ZINC001271719982 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271719982 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 100) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719982 none O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 13, 13, 13, 13, 13, 19, 41, 41, 41, 41, 13, 13, 13, 13, 13, 1, 1, 1, 9, 9, 13, 13, 13, 13, 41, 41, 41, 41, 41, 41, 41, 41, 41, 13, 13, 13, 13, 9, 9, 9, 9, 9] 48 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 101) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@]([O-])([SiH3])C1CC1) `ZINC001271719982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001271719982 none O=C(N1C[C@H]2CN(C3CCCC3)C[C@@H](C1)O2)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 5, 12, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 10, 10, 10, 10, 10, 14, 28, 28, 28, 28, 10, 10, 10, 10, 10, 1, 1, 1, 9, 9, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 10, 10, 10, 10, 9, 9, 9, 9, 9] 38 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719982 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719982 Building ZINC001271720194 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271720194 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/102 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/103 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/103' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/104 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/104' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/105 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/105' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720194 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 Building ZINC001271720194 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271720194 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 102) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 103) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 104) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 105) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720194 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 Building ZINC001271720194 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271720194 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 102) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 103) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 104) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 105) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720194 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 Building ZINC001271720194 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271720194 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 102) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 103) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 26, 42, 24, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 4, 4, 12, 42, 42, 42, 42, 42, 42, 26, 26, 24, 24, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 4, 4, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 104) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 105) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2) `ZINC001271720194.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271720194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720194 none CN(C)CCN1CC2(C1)CCCN(C(=O)[C@]([O-])([SiH3])C1CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 42, 27, 12, 12, 12, 12, 12, 12, 12, 12, 9, 2, 11, 1, 1, 1, 3, 3, 12, 42, 42, 42, 42, 42, 42, 29, 29, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720194 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720194 Building ZINC001271720349 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271720349 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/106 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271720349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271720349 none CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 35, 17, 35, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 48, 48, 35, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/107 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271720349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271720349 none CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 47, 39, 17, 39, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 7, 7, 47, 47, 47, 47, 47, 47, 47, 39, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720349 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 Building ZINC001271720349 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271720349 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 106) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271720349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271720349 none CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 48, 35, 17, 35, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 1, 11, 1, 1, 1, 6, 6, 48, 48, 48, 48, 48, 48, 48, 35, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 107) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/107: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271720349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001271720349 none CC(C)NC(=O)N1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 8, 1, 11, 8, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 39, 47, 39, 17, 39, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1, 12, 1, 1, 1, 7, 7, 47, 47, 47, 47, 47, 47, 47, 39, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720349 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720349 Building ZINC001271720354 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271720354 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/108 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])C1CC1)CC2) `ZINC001271720354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720354 none CN(C)CCN1CC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])C1CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 34, 46, 32, 20, 20, 20, 20, 20, 20, 19, 9, 2, 11, 1, 1, 1, 4, 4, 20, 20, 46, 46, 46, 46, 46, 46, 34, 34, 32, 32, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 20, 20, 20, 20] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/109 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCN(C(=O)[C@]([O-])([SiH3])C1CC1)CC2) `ZINC001271720354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720354 none CN(C)CCN1CC2(C1)CCN(C(=O)[C@]([O-])([SiH3])C1CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 32, 45, 30, 18, 18, 18, 18, 18, 18, 18, 7, 2, 9, 1, 1, 1, 3, 3, 18, 18, 45, 45, 45, 45, 45, 45, 32, 32, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720354 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 Building ZINC001271720354 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271720354 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 108) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])C1CC1)CC2) `ZINC001271720354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271720354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720354 none CN(C)CCN1CC2(C1)CCN(C(=O)[C@@]([O-])([SiH3])C1CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 34, 46, 32, 20, 20, 20, 20, 20, 20, 19, 9, 2, 11, 1, 1, 1, 4, 4, 20, 20, 46, 46, 46, 46, 46, 46, 34, 34, 32, 32, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 20, 20, 20, 20] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 109) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CCN(C(=O)[C@]([O-])([SiH3])C1CC1)CC2) `ZINC001271720354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271720354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001271720354 none CN(C)CCN1CC2(C1)CCN(C(=O)[C@]([O-])([SiH3])C1CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 32, 45, 30, 18, 18, 18, 18, 18, 18, 18, 7, 2, 9, 1, 1, 1, 3, 3, 18, 18, 45, 45, 45, 45, 45, 45, 32, 32, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271720354 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271720354 Building ZINC001271719080 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719080 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/110 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/111 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/111' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/112 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/112' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/113 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/113' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719080 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 Building ZINC001271719080 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719080 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 110) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 111) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 112) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 113) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719080 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 Building ZINC001271719080 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719080 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 110) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 111) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 112) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 113) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719080 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 Building ZINC001271719080 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271719080 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 110) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 111) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 48, 34, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 10, 1, 13, 1, 1, 1, 4, 4, 48, 48, 48, 48, 48, 48, 34, 34, 34, 34, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 112) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/112: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 113) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/113: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1) `ZINC001271719080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271719080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271719080 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 32, 46, 32, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 1, 12, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46, 32, 32, 32, 32, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 4, 4, 4] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271719080 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271719080 Building ZINC000487489574 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489574 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/114 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C) `ZINC000487489574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489574 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [32, 23, 15, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 32, 32, 32, 23, 23, 15, 15, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/115 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C) `ZINC000487489574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489574 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [34, 24, 15, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 16, 16, 16, 16, 16, 34, 34, 34, 24, 24, 15, 15, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 154 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489574 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 Building ZINC000487489574 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489574 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 114) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C) `ZINC000487489574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489574 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [32, 23, 15, 6, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 9, 19, 19, 19, 19, 19, 19, 19, 32, 32, 32, 23, 23, 15, 15, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 152 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 115) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C) `ZINC000487489574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489574 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [34, 24, 15, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 16, 16, 16, 16, 16, 16, 16, 34, 34, 34, 24, 24, 15, 15, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16] 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]) total number of confs: 154 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489574 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489574 Building ZINC000487489575 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489575 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/116 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C) `ZINC000487489575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489575 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [35, 24, 15, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 24, 24, 15, 15, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 154 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/117 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C) `ZINC000487489575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489575 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [34, 23, 15, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 19, 19, 19, 19, 19, 19, 19, 34, 34, 34, 23, 23, 15, 15, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 153 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489575 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 Building ZINC000487489575 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489575 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 116) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C) `ZINC000487489575.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489575 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [35, 24, 15, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 15, 15, 15, 35, 35, 35, 24, 24, 15, 15, 4, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 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]) total number of confs: 154 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 117) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C) `ZINC000487489575.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489575 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [34, 23, 15, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 19, 19, 19, 19, 19, 19, 19, 34, 34, 34, 23, 23, 15, 15, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 153 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489575 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489575 Building ZINC000487489577 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489577 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/118 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C) `ZINC000487489577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489577 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [35, 26, 17, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 26, 26, 17, 17, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 161 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/119 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C) `ZINC000487489577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489577 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 19, 14, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 12, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 19, 19, 14, 14, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 135 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489577 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 Building ZINC000487489577 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489577 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 118) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C) `ZINC000487489577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489577 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [35, 26, 17, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 20, 20, 20, 20, 20, 20, 20, 35, 35, 35, 26, 26, 17, 17, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 161 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 119) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C) `ZINC000487489577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489577 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@H]1CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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, 19, 14, 9, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 12, 21, 21, 21, 21, 21, 21, 21, 30, 30, 30, 19, 19, 14, 14, 5, 5, 5, 5, 5, 5, 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]) total number of confs: 135 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489577 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489577 Building ZINC000487489578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/120 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C) `ZINC000487489578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489578 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [33, 17, 12, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 17, 17, 12, 12, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 125 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/121 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C) `ZINC000487489578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489578 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [32, 24, 16, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 19, 19, 19, 19, 19, 19, 19, 32, 32, 32, 24, 24, 16, 16, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 Building ZINC000487489578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487489578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 120) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C) `ZINC000487489578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487489578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489578 none COCCN(C(=O)[C@@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [33, 17, 12, 8, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 11, 17, 17, 17, 17, 17, 17, 17, 33, 33, 33, 17, 17, 12, 12, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17] 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]) total number of confs: 125 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 121) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C) `ZINC000487489578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487489578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000487489578 none COCCN(C(=O)[C@]([O-])([SiH3])c1cccn1C)[C@@H]1CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 7, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 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: [32, 24, 16, 10, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 13, 19, 19, 19, 19, 19, 19, 19, 32, 32, 32, 24, 24, 16, 16, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19] 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]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487489578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487489578 Building ZINC000614766090 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614766090 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/122 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1) `ZINC000614766090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614766090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000614766090 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', '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, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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: [5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 5, 13, 27, 13, 13, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 27, 27, 81, 13, 13, 13, 13] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 219 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/123 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/123' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1) `ZINC000614766090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614766090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000614766090 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', '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, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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: [5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 5, 13, 27, 13, 13, 5, 5, 5, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 27, 27, 81, 13, 13, 13, 13] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614766090 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 Building ZINC000614766090 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614766090 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 122) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1) `ZINC000614766090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614766090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000614766090 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', '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, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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: [5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 5, 13, 27, 13, 13, 5, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 27, 27, 81, 13, 13, 13, 13] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 219 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 123) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1) `ZINC000614766090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614766090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000614766090 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', '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, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 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: [5, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 12, 12, 12, 4, 5, 13, 27, 13, 13, 5, 5, 5, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 27, 27, 81, 13, 13, 13, 13] 150 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 218 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614766090 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614766090 Building ZINC000614770403 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614770403 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/124 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1) `ZINC000614770403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614770403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000614770403 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 25, 10, 10, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 4, 25, 25, 75, 10, 10, 10, 10, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/125 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/125' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1) `ZINC000614770403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614770403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000614770403 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 24, 10, 10, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 4, 24, 24, 72, 10, 10, 10, 10, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614770403 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 Building ZINC000614770403 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614770403 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 124) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1) `ZINC000614770403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614770403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000614770403 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 25, 10, 10, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 4, 25, 25, 75, 10, 10, 10, 10, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 125) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1) `ZINC000614770403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614770403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000614770403 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)C2(CO)CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 10, 24, 10, 10, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 4, 24, 24, 72, 10, 10, 10, 10, 4] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614770403 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614770403 Building ZINC000617897873 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617897873 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/126 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(CO)CC1) `ZINC000617897873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617897873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000617897873 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 32, 44, 32, 32, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 44, 44, 132, 32, 32, 32, 32] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/127 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/127' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C1(CO)CC1) `ZINC000617897873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617897873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000617897873 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [12, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 31, 42, 31, 31, 12, 12, 12, 4, 5, 5, 5, 5, 5, 5, 42, 42, 126, 31, 31, 31, 31] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 293 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000617897873 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 Building ZINC000617897873 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617897873 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 126) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(CO)CC1) `ZINC000617897873.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617897873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000617897873 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [11, 4, 11, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 11, 32, 44, 32, 32, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 44, 44, 132, 32, 32, 32, 32] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 300 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 127) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C1(CO)CC1) `ZINC000617897873.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617897873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000617897873 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [12, 4, 12, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 12, 31, 42, 31, 31, 12, 12, 12, 4, 5, 5, 5, 5, 5, 5, 42, 42, 126, 31, 31, 31, 31] 150 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 293 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000617897873 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000617897873 Building ZINC000614771015 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614771015 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/128 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1) `ZINC000614771015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614771015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000614771015 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 29, 46, 29, 29, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 46, 46, 138, 29, 29, 29, 29] 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]) total number of confs: 314 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/129 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1) `ZINC000614771015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614771015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000614771015 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 30, 44, 30, 30, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 44, 44, 132, 30, 30, 30, 30] 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]) total number of confs: 299 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614771015 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 Building ZINC000614771015 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000614771015 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 128) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1) `ZINC000614771015.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000614771015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000614771015 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 7, 7, 29, 46, 29, 29, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 46, 46, 138, 29, 29, 29, 29] 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]) total number of confs: 314 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 129) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1) `ZINC000614771015.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000614771015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000614771015 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N(C)C1(CO)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 4, 2, 4, 4, 1, 1, 1, 1, 4, 4, 6, 6, 30, 44, 30, 30, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 44, 44, 132, 30, 30, 30, 30] 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]) total number of confs: 299 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000614771015 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000614771015 Building ZINC000428362687 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428362687 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/130 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1) `ZINC000428362687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428362687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362687 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/131 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1) `ZINC000428362687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428362687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362687 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 2, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428362687 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 Building ZINC000428362687 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428362687 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 130) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1) `ZINC000428362687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428362687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362687 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 131) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1) `ZINC000428362687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428362687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362687 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 2, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428362687 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362687 Building ZINC000428362688 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428362688 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/132 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1) `ZINC000428362688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428362688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362688 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 2, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/133 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1) `ZINC000428362688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428362688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362688 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428362688 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 Building ZINC000428362688 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428362688 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 132) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1) `ZINC000428362688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428362688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362688 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 15, 15, 15, 15, 15, 6, 2, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 133) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1) `ZINC000428362688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428362688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428362688 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H]2CCn3ccnc3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 1, 8, 1, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 20, 20, 20, 20, 20, 7, 3, 12, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428362688 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428362688 Building ZINC000937578106 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937578106 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/134 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC000937578106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937578106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000937578106 none CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 30, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/135 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC000937578106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937578106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000937578106 none CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 13, 13, 13, 13, 13, 4, 1, 7, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 29, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937578106 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 Building ZINC000937578106 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937578106 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 134) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC000937578106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937578106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000937578106 none CCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 30, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 135) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC000937578106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937578106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000937578106 none CCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 13, 13, 13, 13, 13, 4, 1, 7, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 29, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937578106 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937578106 Building ZINC000629244891 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000629244891 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/136 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O) `ZINC000629244891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000629244891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000629244891 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 20, 43, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 132] 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]) total number of confs: 253 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/137 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O) `ZINC000629244891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000629244891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000629244891 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 20, 45, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 138] 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]) total number of confs: 262 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000629244891 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 Building ZINC000629244891 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000629244891 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 136) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O) `ZINC000629244891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000629244891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000629244891 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 20, 43, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 132] 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]) total number of confs: 253 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 137) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O) `ZINC000629244891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000629244891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000629244891 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCOC[C@H]1O NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 20, 45, 46, 46, 46, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 9, 46, 46, 46, 46, 46, 46, 138] 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]) total number of confs: 262 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000629244891 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000629244891 Building ZINC000487501235 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487501235 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/138 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1) `ZINC000487501235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487501235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501235 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 12, 21, 7, 7, 7, 7, 6, 6, 20, 20, 20, 20, 20, 6, 3, 8, 8, 12, 12, 21, 21, 21, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/139 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1) `ZINC000487501235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487501235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501235 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 9, 11, 20, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 4, 9, 9, 11, 11, 20, 20, 20, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487501235 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 Building ZINC000487501235 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487501235 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 138) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1) `ZINC000487501235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487501235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501235 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 12, 21, 7, 7, 7, 7, 6, 6, 20, 20, 20, 20, 20, 6, 3, 8, 8, 12, 12, 21, 21, 21, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 139) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1) `ZINC000487501235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487501235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501235 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 8, 9, 11, 20, 8, 8, 8, 8, 6, 6, 15, 15, 15, 15, 15, 6, 4, 9, 9, 11, 11, 20, 20, 20, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487501235 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501235 Building ZINC000487501251 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487501251 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/140 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1) `ZINC000487501251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487501251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501251 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 11, 20, 7, 7, 7, 7, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 11, 11, 20, 20, 20, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/141 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1) `ZINC000487501251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487501251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501251 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 12, 21, 7, 7, 7, 7, 6, 6, 20, 20, 20, 20, 20, 6, 3, 8, 8, 12, 12, 21, 21, 21, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487501251 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 Building ZINC000487501251 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487501251 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 140) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1) `ZINC000487501251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487501251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501251 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 11, 20, 7, 7, 7, 7, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 11, 11, 20, 20, 20, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 141) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1) `ZINC000487501251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487501251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000487501251 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@]2(CCOC)CCOC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 12, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 7, 8, 12, 21, 7, 7, 7, 7, 6, 6, 20, 20, 20, 20, 20, 6, 3, 8, 8, 12, 12, 21, 21, 21, 7, 7, 7, 7, 7, 7, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487501251 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487501251 Building ZINC000937584286 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937584286 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/142 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/142' -> `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](NC(=O)C2CC2)C1) `ZINC000937584286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937584286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000937584286 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 21, 21, 21, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/143 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/143' -> `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](NC(=O)C2CC2)C1) `ZINC000937584286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937584286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000937584286 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 18, 18, 18, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937584286 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 Building ZINC000937584286 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937584286 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 142) grep: /scratch/xiaobo/365617/xds-8058088.97/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(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1) `ZINC000937584286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937584286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000937584286 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 11, 11, 11, 11, 11, 21, 21, 21, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 143) grep: /scratch/xiaobo/365617/xds-8058088.97/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(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1) `ZINC000937584286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937584286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000937584286 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C2CC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 8, 10, 10, 10, 10, 10, 18, 18, 18, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 18, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937584286 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937584286 Building ZINC000428365824 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428365824 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/144 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1) `ZINC000428365824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428365824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000428365824 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 6, 14, 14, 14, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/145 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1) `ZINC000428365824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428365824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000428365824 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 15, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428365824 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 Building ZINC000428365824 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428365824 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 144) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1) `ZINC000428365824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428365824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000428365824 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 14, 14, 6, 6, 1, 1, 1, 1, 4, 6, 14, 14, 14, 14, 14, 14, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 14, 14, 14, 14, 14, 14, 14, 14, 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 145) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1) `ZINC000428365824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428365824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000428365824 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 14, 7, 7, 1, 1, 1, 1, 4, 6, 15, 15, 15, 15, 15, 15, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 15, 15, 15, 15, 15, 15, 15, 15, 7] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428365824 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428365824 Building ZINC000840919421 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840919421 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/146 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CNC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840919421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840919421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000840919421 none CCN(CC)C(=O)CNC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 29, 33, 36, 13, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36, 13, 13, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/147 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)CNC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840919421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840919421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000840919421 none CCN(CC)C(=O)CNC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 33, 36, 39, 13, 33, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 46, 46, 46, 46, 46, 39, 39, 39, 39, 39, 13, 13, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840919421 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 Building ZINC000840919421 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840919421 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 146) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C(=O)CNC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840919421.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840919421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000840919421 none CCN(CC)C(=O)CNC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 29, 33, 36, 13, 29, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 43, 43, 43, 36, 36, 36, 36, 36, 13, 13, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 200 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 147) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C(=O)CNC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840919421.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840919421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000840919421 none CCN(CC)C(=O)CNC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 36, 33, 36, 39, 13, 33, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 46, 46, 46, 46, 46, 39, 39, 39, 39, 39, 13, 13, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840919421 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840919421 Building ZINC000840922837 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922837 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/148 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922837 none CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 30, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/149 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922837 none CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 12, 31, 5, 1, 5, 1, 1, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840922837 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 Building ZINC000840922837 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840922837 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 148) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840922837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922837 none CN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 30, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 149) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840922837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840922837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840922837 none CN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 12, 31, 5, 1, 5, 1, 1, 2, 8, 8, 8, 8, 8, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 93 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840922837 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840922837 Building ZINC000840923572 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840923572 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/150 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840923572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840923572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923572 none COCCOC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 41, 31, 18, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 45, 45, 41, 41, 18, 18, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/151 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840923572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840923572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923572 none COCCOC[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens 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, 42, 40, 28, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 43, 43, 43, 42, 42, 40, 40, 16, 16, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840923572 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 Building ZINC000840923572 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840923572 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 150) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840923572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840923572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923572 none COCCOC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 45, 41, 31, 18, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 46, 46, 46, 45, 45, 41, 41, 18, 18, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 151) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOC[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840923572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840923572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923572 none COCCOC[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens 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, 42, 40, 28, 16, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 43, 43, 43, 42, 42, 40, 40, 16, 16, 8, 8, 8, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840923572 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923572 Building ZINC000840923573 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840923573 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/152 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840923573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840923573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923573 none COCCOC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens 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, 41, 41, 29, 18, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 41, 41, 41, 41, 18, 18, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/153 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840923573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840923573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923573 none COCCOC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 43, 29, 15, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 43, 43, 15, 15, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840923573 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 Building ZINC000840923573 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840923573 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 152) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840923573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840923573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923573 none COCCOC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens 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, 41, 41, 29, 18, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 41, 41, 41, 41, 18, 18, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 153) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840923573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840923573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840923573 none COCCOC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 43, 29, 15, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 43, 43, 15, 15, 8, 8, 8, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840923573 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840923573 Building ZINC000840924445 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840924445 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/154 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840924445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840924445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000840924445 none CC(C)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [40, 22, 40, 22, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 22, 22, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/155 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840924445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840924445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000840924445 none CC(C)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [43, 24, 43, 24, 24, 24, 7, 24, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840924445 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 Building ZINC000840924445 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840924445 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 154) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840924445.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840924445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000840924445 none CC(C)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [40, 22, 40, 22, 22, 22, 8, 22, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 22, 22, 40, 40, 40, 40, 40, 40, 40, 22, 22, 22, 22, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 155) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O) `ZINC000840924445.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840924445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000840924445 none CC(C)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [43, 24, 43, 24, 24, 24, 7, 24, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 24, 24, 43, 43, 43, 43, 43, 43, 43, 24, 24, 24, 24, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840924445 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840924445 Building ZINC000840926727 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926727 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/156 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]21) `ZINC000840926727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926727 none COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 2, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/157 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]21) `ZINC000840926727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926727 none COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 2, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926727 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 Building ZINC000840926727 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926727 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 156) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]21) `ZINC000840926727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926727 none COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 2, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 157) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]21) `ZINC000840926727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926727 none COC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 10, 30, 10, 10, 10, 10, 10, 4, 1, 4, 1, 1, 2, 5, 5, 5, 5, 5, 10, 10, 10, 30, 30, 30, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926727 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926727 Building ZINC000840926483 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926483 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/158 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840926483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926483 none C[C@@H](CN(C)C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 15, 30, 30, 30, 5, 1, 5, 1, 1, 2, 6, 6, 6, 6, 6, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/159 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/159' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840926483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926483 none C[C@@H](CN(C)C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 4, 18, 18, 35, 35, 35, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926483 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 Building ZINC000840926483 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926483 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 158) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/158: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840926483.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926483 none C[C@@H](CN(C)C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 15, 30, 30, 30, 5, 1, 5, 1, 1, 2, 6, 6, 6, 6, 6, 15, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 134 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 159) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/159: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CN(C)C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840926483.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926483 none C[C@@H](CN(C)C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 4, 18, 18, 35, 35, 35, 4, 1, 4, 1, 1, 2, 6, 6, 6, 6, 6, 18, 18, 18, 35, 35, 35, 35, 35, 35, 35, 35, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926483 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926483 Building ZINC000840926495 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926495 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/160 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840926495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926495 none CC1(C)[C@H](O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 10, 24, 6, 1, 6, 1, 1, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 72, 24, 24, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9] 150 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/161 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/161' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840926495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926495 none CC1(C)[C@H](O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 2, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 84, 28, 28, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926495 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 Building ZINC000840926495 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840926495 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 160) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1(C)[C@H](O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840926495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840926495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926495 none CC1(C)[C@H](O)C[C@H]1NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 10, 24, 6, 1, 6, 1, 1, 2, 9, 9, 9, 9, 9, 24, 24, 24, 24, 24, 24, 72, 24, 24, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9] 150 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 161) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1(C)[C@H](O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840926495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840926495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840926495 none CC1(C)[C@H](O)C[C@H]1NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 10, 28, 6, 1, 6, 1, 1, 2, 11, 11, 11, 11, 11, 28, 28, 28, 28, 28, 28, 84, 28, 28, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11] 150 rigid atoms, others: [10, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 181 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840926495 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840926495 Building ZINC000840927101 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927101 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/162 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1) `ZINC000840927101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000840927101 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 9, 1, 15, 1, 1, 2, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/163 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/163' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1) `ZINC000840927101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000840927101 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 11, 1, 16, 1, 1, 2, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927101 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 Building ZINC000840927101 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927101 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 162) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1) `ZINC000840927101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000840927101 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 9, 1, 15, 1, 1, 2, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 10, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29] 50 rigid atoms, others: [9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 163) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1) `ZINC000840927101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000840927101 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C3CCSCC3)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 11, 1, 16, 1, 1, 2, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927101 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927101 Building ZINC000840927422 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927422 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/164 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927422 none CCN(C)C(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 24, 17, 24, 8, 17, 4, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 24, 24, 24, 8, 8, 8, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/165 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/165' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927422 none CCN(C)C(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 21, 32, 9, 21, 3, 9, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 32, 32, 32, 9, 9, 9, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927422 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 Building ZINC000840927422 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927422 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 164) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927422 none CCN(C)C(=O)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 24, 17, 24, 8, 17, 4, 8, 8, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 35, 35, 35, 35, 35, 24, 24, 24, 8, 8, 8, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 154 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 165) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927422 none CCN(C)C(=O)[C@@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 32, 21, 32, 9, 21, 3, 9, 9, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 41, 41, 41, 41, 41, 32, 32, 32, 9, 9, 9, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 170 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927422 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927422 Building ZINC000840927425 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927425 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/166 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927425 none CCN(C)C(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 33, 22, 33, 7, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 33, 33, 33, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/167 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927425 none CCN(C)C(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 14, 22, 7, 14, 3, 7, 7, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 22, 22, 22, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927425 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 Building ZINC000840927425 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840927425 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 166) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1) `ZINC000840927425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840927425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927425 none CCN(C)C(=O)[C@H](C)NC(=O)[C@@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens 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, 33, 22, 33, 7, 22, 3, 7, 7, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 40, 40, 40, 40, 40, 33, 33, 33, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 162 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 167) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1) `ZINC000840927425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840927425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000840927425 none CCN(C)C(=O)[C@H](C)NC(=O)[C@]([O-])([SiH3])C1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 22, 14, 22, 7, 14, 3, 7, 7, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 22, 22, 22, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840927425 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840927425 Building ZINC000108214396 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108214396 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/168 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1) `ZINC000108214396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108214396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000108214396 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 11, 25, 25, 33, 33, 33, 33, 33, 9, 9, 9, 3, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/169 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1) `ZINC000108214396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108214396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000108214396 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 24, 24, 34, 34, 34, 34, 34, 9, 9, 9, 4, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000108214396 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 Building ZINC000108214396 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108214396 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 168) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1) `ZINC000108214396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108214396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000108214396 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 1, 3, 1, 1, 1, 10, 10, 10, 10, 10, 11, 25, 25, 33, 33, 33, 33, 33, 9, 9, 9, 3, 10, 10, 10, 10, 10, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 169) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1) `ZINC000108214396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108214396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000108214396 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 10, 24, 24, 34, 34, 34, 34, 34, 9, 9, 9, 4, 9, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000108214396 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000108214396 Building ZINC000304934578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304934578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/170 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O) `ZINC000304934578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304934578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934578 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 10, 30, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 30, 30, 41, 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]) total number of confs: 297 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/171 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O) `ZINC000304934578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304934578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934578 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 31, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 31, 31, 43, 43, 43, 129] 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]) total number of confs: 311 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304934578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 Building ZINC000304934578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304934578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 170) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/170: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O) `ZINC000304934578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304934578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934578 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 10, 10, 30, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 30, 30, 41, 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]) total number of confs: 297 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 171) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/171: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O) `ZINC000304934578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304934578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934578 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 31, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 31, 31, 43, 43, 43, 129] 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]) total number of confs: 311 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304934578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934578 Building ZINC000305080146 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305080146 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/172 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCO) `ZINC000305080146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305080146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080146 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 13, 32, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 35, 35, 40, 42, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/173 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/173' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCO) `ZINC000305080146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305080146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080146 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 30, 40, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 32, 32, 40, 39, 43, 43, 129] 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]) total number of confs: 330 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305080146 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 Building ZINC000305080146 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305080146 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 172) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCO) `ZINC000305080146.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305080146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080146 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 13, 32, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 35, 35, 40, 42, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 173) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCO) `ZINC000305080146.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305080146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080146 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 30, 40, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 13, 13, 13, 32, 32, 40, 39, 43, 43, 129] 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]) total number of confs: 330 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305080146 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080146 Building ZINC000305080148 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305080148 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/174 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO) `ZINC000305080148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305080148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080148 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 15, 34, 41, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 15, 15, 15, 36, 36, 41, 40, 43, 43, 129] 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]) total number of confs: 323 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/175 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO) `ZINC000305080148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305080148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080148 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 13, 32, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 35, 35, 42, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305080148 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 Building ZINC000305080148 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305080148 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 174) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/174: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO) `ZINC000305080148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305080148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080148 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 15, 34, 41, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 15, 15, 15, 36, 36, 41, 40, 43, 43, 129] 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]) total number of confs: 323 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 175) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/175: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO) `ZINC000305080148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305080148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305080148 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 12, 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, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 13, 13, 13, 32, 42, 47, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 13, 13, 13, 35, 35, 42, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 363 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305080148 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305080148 Building ZINC000840928955 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840928955 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/176 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840928955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928955 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 30, 30, 30, 30, 30, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/177 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840928955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928955 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 34, 34, 34, 34, 34, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840928955 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 Building ZINC000840928955 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840928955 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 176) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928955.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840928955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928955 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [30, 16, 16, 16, 6, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 30, 30, 30, 30, 30, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 177) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928955.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840928955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928955 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 18, 18, 18, 5, 18, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 18, 18, 18, 34, 34, 34, 34, 34, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840928955 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928955 Building ZINC000840928956 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840928956 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/178 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840928956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928956 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/179 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840928956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928956 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 19, 19, 19, 6, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 35, 35, 35, 35, 35, 19, 19, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840928956 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 Building ZINC000840928956 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000840928956 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 178) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000840928956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928956 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 16, 5, 16, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 16, 31, 31, 31, 31, 31, 16, 16, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 179) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O) `ZINC000840928956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000840928956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000840928956 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])C2CCSCC2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 14, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [35, 19, 19, 19, 6, 19, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 19, 19, 19, 35, 35, 35, 35, 35, 19, 19, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000840928956 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000840928956 Building ZINC000305130865 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305130865 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/180 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C(C)C) `ZINC000305130865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305130865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130865 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 17, 17, 33, 39, 17, 36, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 39, 39, 117, 37, 37, 37, 37, 37, 37, 37] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 400 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/181 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCO)C(C)C) `ZINC000305130865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305130865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130865 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 21, 21, 36, 42, 21, 35, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 42, 42, 126, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 415 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305130865 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 Building ZINC000305130865 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305130865 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 180) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/180: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C(C)C) `ZINC000305130865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305130865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130865 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 6, 6, 6, 17, 17, 33, 39, 17, 36, 37, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 34, 34, 39, 39, 117, 37, 37, 37, 37, 37, 37, 37] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 400 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 181) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/181: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCO)C(C)C) `ZINC000305130865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305130865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130865 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 21, 21, 36, 42, 21, 35, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 42, 42, 126, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 415 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305130865 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130865 Building ZINC000305130866 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305130866 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/182 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(C)C) `ZINC000305130866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305130866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130866 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 21, 21, 36, 42, 21, 38, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 42, 42, 126, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 415 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/183 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(C)C) `ZINC000305130866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305130866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130866 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 16, 16, 32, 38, 16, 34, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 33, 33, 38, 38, 114, 34, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 375 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305130866 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 Building ZINC000305130866 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305130866 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 182) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(C)C) `ZINC000305130866.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305130866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130866 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 21, 21, 36, 42, 21, 38, 35, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 37, 37, 42, 42, 126, 38, 38, 38, 38, 38, 38, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 415 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 183) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(C)C) `ZINC000305130866.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305130866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000305130866 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C(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', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 16, 16, 32, 38, 16, 34, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 33, 33, 38, 38, 114, 34, 34, 34, 34, 34, 34, 34] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 375 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305130866 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305130866 Building ZINC000305186909 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305186909 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/184 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCO) `ZINC000305186909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305186909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186909 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 40, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 40, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/185 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCO) `ZINC000305186909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305186909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186909 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 42, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 42, 42, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305186909 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 Building ZINC000305186909 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305186909 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 184) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/184: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCO) `ZINC000305186909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305186909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186909 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 40, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 40, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 185) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/185: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCO) `ZINC000305186909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305186909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186909 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 42, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 42, 42, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 352 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305186909 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186909 Building ZINC000305186910 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305186910 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/186 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCO) `ZINC000305186910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305186910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186910 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 43, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 43, 43, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 355 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/187 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/187' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCO) `ZINC000305186910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305186910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186910 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 40, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 40, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305186910 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 Building ZINC000305186910 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305186910 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 186) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/186: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCO) `ZINC000305186910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305186910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186910 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 43, 48, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 43, 43, 48, 48, 144] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 355 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 187) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/187: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCO) `ZINC000305186910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305186910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305186910 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)CCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 7, 7, 7, 23, 23, 23, 40, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 23, 23, 23, 40, 40, 47, 47, 141] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 343 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305186910 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305186910 Building ZINC000347337819 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347337819 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/188 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1) `ZINC000347337819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347337819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347337819 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/189 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1) `ZINC000347337819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347337819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347337819 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000347337819 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 Building ZINC000347337819 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347337819 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 188) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1) `ZINC000347337819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347337819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347337819 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 18, 18, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 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]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 189) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1) `ZINC000347337819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347337819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000347337819 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cc(C)nc(C)n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 5, 8, 1, 5, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 19, 19, 19, 19, 19, 19, 19, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 19, 19, 19, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000347337819 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347337819 Building ZINC000347338993 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347338993 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/190 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1) `ZINC000347338993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347338993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347338993 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 6, 6, 6, 6, 6, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/191 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1) `ZINC000347338993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347338993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347338993 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 6, 6, 6, 6, 6, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000347338993 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 Building ZINC000347338993 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000347338993 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 190) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/190: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1) `ZINC000347338993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000347338993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347338993 none Cc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 13, 13, 2, 6, 6, 6, 6, 6, 30, 30, 30] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 191) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/191: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1) `ZINC000347338993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000347338993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000347338993 none Cc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)nc(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 1, 5, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 13, 13, 2, 6, 6, 6, 6, 6, 29, 29, 29] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000347338993 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000347338993 Building ZINC000305666756 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305666756 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/192 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1) `ZINC000305666756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305666756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666756 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 12, 14, 7, 10, 10, 6, 6, 19, 19, 19, 19, 19, 6, 3, 14, 14, 14, 14, 42, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/193 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/193' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1) `ZINC000305666756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305666756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666756 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 14, 8, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 3, 14, 14, 14, 14, 42, 11, 11, 11, 11, 11, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305666756 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 Building ZINC000305666756 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305666756 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 192) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1) `ZINC000305666756.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305666756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666756 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [19, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 12, 14, 7, 10, 10, 6, 6, 19, 19, 19, 19, 19, 6, 3, 14, 14, 14, 14, 42, 10, 10, 10, 10, 10, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 193) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1) `ZINC000305666756.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305666756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666756 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [20, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 12, 14, 8, 11, 11, 7, 7, 20, 20, 20, 20, 20, 7, 3, 14, 14, 14, 14, 42, 11, 11, 11, 11, 11, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305666756 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666756 Building ZINC000305666758 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305666758 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/194 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1) `ZINC000305666758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305666758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666758 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 13, 8, 12, 12, 7, 7, 21, 21, 21, 21, 21, 7, 3, 13, 13, 13, 13, 39, 12, 12, 12, 12, 12, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/195 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1) `ZINC000305666758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305666758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666758 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 14, 7, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 3, 13, 13, 14, 14, 42, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305666758 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 Building ZINC000305666758 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305666758 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 194) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1) `ZINC000305666758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305666758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666758 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 13, 8, 12, 12, 7, 7, 21, 21, 21, 21, 21, 7, 3, 13, 13, 13, 13, 39, 12, 12, 12, 12, 12, 7] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 191 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 195) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1) `ZINC000305666758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305666758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305666758 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCO)C2CC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 14, 7, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 3, 13, 13, 14, 14, 42, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 174 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305666758 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305666758 Building ZINC000305678878 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305678878 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/196 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1) `ZINC000305678878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305678878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678878 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/197 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1) `ZINC000305678878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305678878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678878 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 14, 14, 14, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 14, 14, 14, 42, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305678878 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 Building ZINC000305678878 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305678878 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 196) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1) `ZINC000305678878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305678878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678878 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 17, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 197) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1) `ZINC000305678878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305678878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678878 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 14, 14, 14, 16, 16, 6, 6, 18, 18, 18, 18, 18, 6, 2, 11, 11, 14, 14, 14, 42, 16, 16, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305678878 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678878 Building ZINC000305678879 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305678879 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/198 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1) `ZINC000305678879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305678879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678879 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 5, 5, 14, 14, 14, 14, 14, 5, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/199 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/199' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1) `ZINC000305678879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305678879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678879 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 17, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 6, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305678879 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 Building ZINC000305678879 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305678879 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 198) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1) `ZINC000305678879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305678879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678879 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 5, 5, 14, 14, 14, 14, 14, 5, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 199) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1) `ZINC000305678879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305678879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305678879 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@](C)(O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 17, 18, 18, 18, 18, 6, 6, 14, 14, 14, 14, 14, 6, 2, 12, 12, 18, 18, 18, 54, 18, 18, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305678879 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305678879 Building ZINC001018635078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001018635078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/200 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O) `ZINC001018635078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001018635078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001018635078 none CC[C@@H](N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.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', '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'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 11, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 18, 23, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 23, 47, 47, 37, 37, 37, 37, 37, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/201 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/201' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O) `ZINC001018635078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001018635078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001018635078 none CC[C@@H](N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.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', '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'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 11, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 24, 22, 24, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 24, 40, 40, 47, 47, 47, 47, 47, 22, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 40, 40] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001018635078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 Building ZINC001018635078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001018635078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 200) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O) `ZINC001018635078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001018635078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001018635078 none CC[C@@H](N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.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', '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'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 11, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 23, 18, 23, 6, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 1, 1, 1, 6, 23, 47, 47, 37, 37, 37, 37, 37, 18, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 47, 47] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44]) total number of confs: 226 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 201) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O) `ZINC001018635078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001018635078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001018635078 none CC[C@@H](N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.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', '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'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 11, 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, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 24, 22, 24, 11, 11, 11, 11, 11, 7, 1, 7, 1, 1, 1, 1, 1, 1, 11, 24, 40, 40, 47, 47, 47, 47, 47, 22, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 40, 40] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 12, 13, 14, 15, 16, 17] 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, 41, 42, 43, 44]) total number of confs: 247 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001018635078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001018635078 Building ZINC000305723244 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305723244 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/202 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1) `ZINC000305723244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305723244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305723244 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 13, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/203 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/203' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1) `ZINC000305723244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305723244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305723244 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 2, 12, 12, 48, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305723244 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 Building ZINC000305723244 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305723244 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 202) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1) `ZINC000305723244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305723244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305723244 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 13, 13, 13, 6, 6, 16, 16, 16, 16, 16, 6, 2, 11, 11, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 137 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 203) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1) `ZINC000305723244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305723244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305723244 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)CC(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 12, 16, 16, 16, 17, 17, 17, 6, 6, 18, 18, 18, 18, 18, 6, 2, 12, 12, 48, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305723244 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305723244 Building ZINC000305811578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305811578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/204 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO) `ZINC000305811578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305811578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811578 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 9, 9, 16, 16, 16, 16, 16, 16, 26, 39, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 26, 26, 39, 39, 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]) total number of confs: 294 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/205 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO) `ZINC000305811578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305811578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811578 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 6, 10, 10, 10, 10, 10, 10, 27, 34, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 27, 27, 34, 34, 38, 38, 114] 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]) total number of confs: 278 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305811578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 Building ZINC000305811578 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305811578 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 204) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO) `ZINC000305811578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305811578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811578 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 9, 9, 16, 16, 16, 16, 16, 16, 26, 39, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 26, 26, 39, 39, 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]) total number of confs: 294 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 205) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/205: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO) `ZINC000305811578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305811578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811578 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 6, 10, 10, 10, 10, 10, 10, 27, 34, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 27, 27, 34, 34, 38, 38, 114] 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]) total number of confs: 278 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305811578 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811578 Building ZINC000305811579 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305811579 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/206 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO) `ZINC000305811579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305811579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811579 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 6, 10, 10, 10, 10, 10, 10, 26, 34, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 26, 26, 34, 34, 38, 38, 114] 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]) total number of confs: 278 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/207 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO) `ZINC000305811579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305811579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811579 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 9, 9, 16, 16, 16, 16, 16, 16, 26, 38, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 26, 26, 38, 38, 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]) total number of confs: 295 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305811579 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 Building ZINC000305811579 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305811579 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 206) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/206: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO) `ZINC000305811579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305811579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811579 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 6, 6, 10, 10, 10, 10, 10, 10, 26, 34, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 26, 26, 34, 34, 38, 38, 114] 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]) total number of confs: 278 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 207) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/207: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO) `ZINC000305811579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305811579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000305811579 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1CCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 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, 9, 9, 16, 16, 16, 16, 16, 16, 26, 38, 41, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 26, 26, 38, 38, 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]) total number of confs: 295 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305811579 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305811579 Building ZINC000112916004 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112916004 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/208 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1) `ZINC000112916004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112916004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000112916004 none CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 15, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/209 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1) `ZINC000112916004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112916004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000112916004 none CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 13, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 23, 23, 23, 23, 23, 23, 13, 13, 13, 13, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000112916004 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 Building ZINC000112916004 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000112916004 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 208) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1) `ZINC000112916004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000112916004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000112916004 none CN(C)CCN(C(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 24, 15, 7, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 209) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1) `ZINC000112916004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000112916004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000112916004 none CN(C)CCN(C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 13, 8, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 8, 15, 15, 15, 15, 23, 23, 23, 23, 23, 23, 13, 13, 13, 13, 4, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 103 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000112916004 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000112916004 Building ZINC000113845952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113845952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/210 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113845952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845952 none CC(C)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 23, 23, 23, 23, 23, 23, 23, 19, 2, 19, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/211 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113845952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845952 none CC(C)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113845952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 Building ZINC000113845952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113845952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 210) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113845952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845952 none CC(C)C[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 23, 23, 23, 23, 23, 23, 23, 19, 2, 19, 1, 1, 1, 11, 11, 11, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 211) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113845952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845952 none CC(C)C[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 21, 21, 21, 21, 18, 2, 18, 1, 1, 1, 12, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 92 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113845952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845952 Building ZINC000113845949 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113845949 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/212 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113845949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845949 none CC(C)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 33 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/213 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/213' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113845949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845949 none CC(C)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 12, 2, 12, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10] 31 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113845949 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 Building ZINC000113845949 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113845949 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 212) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845949.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113845949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845949 none CC(C)C[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 11] 33 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 213) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000113845949.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113845949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000113845949 none CC(C)C[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 12, 2, 12, 1, 1, 1, 10, 10, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 14, 14, 14, 14, 10, 10, 10, 10, 10] 31 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 46 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113845949 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113845949 Building ZINC000115302959 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115302959 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/214 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115302959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302959 none CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/215 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115302959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302959 none CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000115302959 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 Building ZINC000115302959 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115302959 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 214) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302959.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115302959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302959 none CC[C@@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 215) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302959.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115302959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302959 none CC[C@@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000115302959 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302959 Building ZINC000115302961 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115302961 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/216 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115302961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302961 none CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/217 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115302961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302961 none CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000115302961 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 Building ZINC000115302961 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115302961 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 216) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115302961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302961 none CC[C@H]1COCCN1C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 10, 2, 10, 1, 1, 1, 10, 10, 10, 10, 10, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 217) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000115302961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115302961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000115302961 none CC[C@H]1COCCN1C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 15, 15, 15, 15, 15, 15, 12, 2, 12, 1, 1, 1, 9, 9, 9, 9, 9, 21, 21, 21, 21, 21, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000115302961 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000115302961 Building ZINC000937604570 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937604570 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/218 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/218' -> `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](NC(=O)C(C)(F)F)C1) `ZINC000937604570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937604570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000937604570 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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, 3, 5, 9, 9, 9, 9, 9, 26, 26, 26, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/219 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/219' -> `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](NC(=O)C(C)(F)F)C1) `ZINC000937604570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937604570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000937604570 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 24, 24, 24, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937604570 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 Building ZINC000937604570 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000937604570 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 218) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1) `ZINC000937604570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000937604570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000937604570 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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, 3, 5, 9, 9, 9, 9, 9, 26, 26, 26, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 26, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 219) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1) `ZINC000937604570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000937604570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000937604570 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)C(C)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 9, 9, 9, 9, 9, 24, 24, 24, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000937604570 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000937604570 Building ZINC000113904820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113904820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/220 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1) `ZINC000113904820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113904820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000113904820 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 6, 35, 35, 35, 35, 35, 35, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/221 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/221' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1) `ZINC000113904820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113904820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000113904820 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 6, 35, 35, 35, 35, 35, 35, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113904820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 Building ZINC000113904820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113904820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 220) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1) `ZINC000113904820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113904820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000113904820 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 6, 35, 35, 35, 35, 35, 35, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 221) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1) `ZINC000113904820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113904820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000113904820 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3c(c2)CC(=O)N3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 6, 35, 35, 35, 35, 35, 35, 11] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113904820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113904820 Building ZINC000444512222 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444512222 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/222 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000444512222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444512222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000444512222 none CC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 4, 10, 10, 18, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 15, 15, 15, 15, 15, 18, 18, 54, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/223 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000444512222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444512222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000444512222 none CC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 3, 10, 10, 20, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 15, 15, 15, 15, 15, 20, 20, 60, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000444512222 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 Building ZINC000444512222 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000444512222 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 222) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000444512222.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000444512222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000444512222 none CC[C@@H](CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 10, 4, 10, 10, 18, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 17, 17, 17, 8, 15, 15, 15, 15, 15, 18, 18, 54, 4, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 223) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000444512222.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000444512222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000444512222 none CC[C@@H](CO)NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 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, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 10, 3, 10, 10, 20, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 15, 15, 15, 15, 15, 20, 20, 60, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000444512222 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000444512222 Building ZINC000353314175 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353314175 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/224 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O) `ZINC000353314175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353314175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000353314175 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 26, 42, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 18, 18, 31, 31, 40, 39, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/225 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O) `ZINC000353314175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353314175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000353314175 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 26, 42, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 18, 18, 31, 31, 39, 40, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000353314175 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 Building ZINC000353314175 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000353314175 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 224) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O) `ZINC000353314175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000353314175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000353314175 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 26, 42, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 18, 18, 31, 31, 40, 39, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 225) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O) `ZINC000353314175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000353314175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000353314175 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCCCN1CCCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 18, 26, 42, 48, 48, 48, 48, 48, 48, 4, 4, 4, 4, 4, 4, 3, 18, 18, 31, 31, 39, 40, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000353314175 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000353314175 Building ZINC000113992287 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113992287 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/226 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000113992287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113992287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000113992287 none CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 30, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 30, 30, 30, 30, 30, 30, 21, 21, 14, 14, 3, 8, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/227 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000113992287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113992287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000113992287 none CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 28, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 28, 28, 28, 28, 28, 28, 21, 21, 14, 14, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113992287 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 Building ZINC000113992287 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000113992287 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 226) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000113992287.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000113992287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000113992287 none CN(C)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 21, 30, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 30, 30, 30, 30, 30, 30, 21, 21, 14, 14, 3, 8, 9, 9, 9, 9, 9, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 227) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000113992287.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000113992287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000113992287 none CN(C)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 28, 14, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 28, 28, 28, 28, 28, 28, 21, 21, 14, 14, 3, 8, 9, 9, 8, 9, 9, 8] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000113992287 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000113992287 Building ZINC000194933046 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194933046 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/228 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1nc(=O)[nH][nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194933046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194933046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194933046 none O=C(NCCCc1nc(=O)[nH][nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 11, 8, 6, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 5, 23, 23, 34, 34, 42, 39, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/229 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCc1nc(=O)[nH][nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194933046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194933046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194933046 none O=C(NCCCc1nc(=O)[nH][nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 11, 8, 6, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 4, 22, 22, 33, 33, 39, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194933046 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 Building ZINC000194933046 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194933046 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 228) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCCCc1nc(=O)[nH][nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194933046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194933046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194933046 none O=C(NCCCc1nc(=O)[nH][nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 11, 8, 6, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 5, 23, 23, 34, 34, 42, 39, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 229) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCCCc1nc(=O)[nH][nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194933046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194933046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000194933046 none O=C(NCCCc1nc(=O)[nH][nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'H', 'N.pl3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 1, 11, 8, 6, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 22, 22, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 3, 3, 1, 3, 3, 4, 22, 22, 33, 33, 39, 42, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194933046 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194933046 Building ZINC000194934271 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194934271 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/230 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(=O)[nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194934271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194934271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000194934271 none O=C(NCc1csc(=O)[nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 11, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 44, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/231 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/231' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1csc(=O)[nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194934271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194934271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000194934271 none O=C(NCc1csc(=O)[nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 11, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 44, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194934271 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 Building ZINC000194934271 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000194934271 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 230) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCc1csc(=O)[nH]1)[C@]([O-])([SiH3])c1ccccc1) `ZINC000194934271.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000194934271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000194934271 none O=C(NCc1csc(=O)[nH]1)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 11, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 44, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 231) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCc1csc(=O)[nH]1)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000194934271.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000194934271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000194934271 none O=C(NCc1csc(=O)[nH]1)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 14, 1, 11, 8, 6, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 6, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 19, 44, 44, 44, 44, 44, 44, 1, 1, 1, 3, 3, 1, 3, 3, 3, 19, 19, 44, 3, 3, 1, 3, 3] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000194934271 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000194934271 Building ZINC000523314214 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523314214 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/232 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523314214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314214 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 29, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 34, 34, 34, 34, 29, 29, 29, 18, 18, 3, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/233 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/233' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523314214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314214 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 31, 33, 33, 33, 33, 31, 31, 31, 18, 18, 4, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523314214 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 Building ZINC000523314214 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523314214 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 232) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314214.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523314214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314214 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 18, 29, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 29, 34, 34, 34, 34, 29, 29, 29, 18, 18, 3, 7, 7, 7, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 233) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314214.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523314214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314214 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 31, 33, 33, 33, 33, 31, 31, 31, 18, 18, 4, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523314214 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314214 Building ZINC000523314215 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523314215 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/234 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523314215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314215 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 31, 33, 33, 33, 33, 31, 31, 31, 18, 18, 4, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/235 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/235' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523314215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314215 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 18, 27, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 27, 30, 30, 30, 30, 27, 27, 27, 18, 18, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523314215 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 Building ZINC000523314215 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523314215 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 234) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523314215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314215 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 31, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 31, 33, 33, 33, 33, 31, 31, 31, 18, 18, 4, 7, 7, 7, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 235) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1) `ZINC000523314215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523314215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000523314215 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 10, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 18, 27, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 27, 30, 30, 30, 30, 27, 27, 27, 18, 18, 3, 9, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523314215 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523314215 Building ZINC000523332801 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332801 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/236 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/237 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/237' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/238 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/238' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/239 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/239' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332801 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 Building ZINC000523332801 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332801 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 236) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 237) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 238) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 239) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332801 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 Building ZINC000523332801 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332801 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 236) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 237) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 238) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 239) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332801 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 Building ZINC000523332801 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332801 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 236) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 237) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 18, 33, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 13, 13, 2, 5, 5, 5, 5, 5, 33, 33] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 238) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/238: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 239) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/239: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332801.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332801 none CC(C)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 18, 31, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332801 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332801 Building ZINC000523332802 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332802 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/240 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/241 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/242 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/242' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/243 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/243' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332802 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 Building ZINC000523332802 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332802 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 240) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 241) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 242) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 243) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332802 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 Building ZINC000523332802 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332802 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 240) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 241) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 242) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 243) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332802 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 Building ZINC000523332802 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000523332802 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 240) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 241) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 18, 30, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 2, 5, 5, 5, 5, 5, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 242) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 243) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/243: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000523332802.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000523332802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000523332802 none CC(C)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 10, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 18, 35, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13, 2, 6, 6, 6, 6, 6, 35, 35] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523332802 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523332802 Building ZINC000195145399 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195145399 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/244 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195145399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145399 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 7, 24, 24, 24, 24, 24, 7, 7, 7, 4, 10, 10, 10, 10, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/245 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195145399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145399 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 8, 8, 8, 4, 8, 8, 8, 8, 8, 28, 28, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195145399 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 Building ZINC000195145399 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195145399 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 244) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/244: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145399.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195145399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145399 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 7, 24, 24, 24, 24, 24, 7, 7, 7, 4, 10, 10, 10, 10, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 245) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/245: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145399.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195145399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145399 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 8, 8, 8, 4, 8, 8, 8, 8, 8, 28, 28, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195145399 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145399 Building ZINC000195145409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195145409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/246 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195145409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145409 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 8, 8, 8, 4, 8, 8, 8, 8, 8, 28, 28, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/247 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/247' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195145409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145409 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 7, 24, 24, 24, 24, 24, 7, 7, 7, 4, 10, 10, 10, 10, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195145409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 Building ZINC000195145409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195145409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 246) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195145409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145409 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28, 28, 28, 28, 8, 8, 8, 4, 8, 8, 8, 8, 8, 28, 28, 28, 28] 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]) total number of confs: 68 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 247) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1) `ZINC000195145409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195145409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000195145409 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 7, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 7, 24, 24, 24, 24, 24, 7, 7, 7, 4, 10, 10, 10, 10, 10, 24, 24, 24, 24] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 60 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195145409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195145409 Building ZINC000195149678 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195149678 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/248 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C) `ZINC000195149678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195149678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000195149678 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 5, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 14, 21, 21, 25, 25, 14, 14, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/249 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/249' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C) `ZINC000195149678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195149678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000195149678 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 6, 15, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 15, 25, 25, 27, 27, 15, 15, 15, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195149678 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 Building ZINC000195149678 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195149678 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 248) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C) `ZINC000195149678.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195149678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000195149678 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 5, 14, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 14, 21, 21, 25, 25, 14, 14, 14, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 249) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C) `ZINC000195149678.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195149678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000195149678 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(=O)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 6, 15, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 15, 25, 25, 27, 27, 15, 15, 15, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195149678 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195149678 Building ZINC000195156557 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156557 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/250 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/251 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/252 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/252' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/253 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/253' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195156557 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 Building ZINC000195156557 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156557 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 250) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 251) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 252) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 253) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195156557 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 Building ZINC000195156557 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156557 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 250) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 251) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 252) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 253) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195156557 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 Building ZINC000195156557 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000195156557 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 250) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 251) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 39, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 252) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 253) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000195156557.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000195156557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000195156557 none C[C@@H]1CCCCN1CCCNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 5, 10, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 42, 42, 37, 16, 12, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 18, 18, 18, 18, 12, 12, 2, 4, 4, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195156557 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195156557 Building ZINC000195285465 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195285465 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/254 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1) `ZINC000195285465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195285465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000195285465 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 16, 16, 11, 16, 16, 16, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 4, 16, 16, 16, 16, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/255 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/255' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1) `ZINC000195285465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195285465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000195285465 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 17, 17, 9, 17, 17, 17, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195285465 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 Building ZINC000195285465 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000195285465 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 254) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/254: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1) `ZINC000195285465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000195285465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000195285465 none Cn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 16, 16, 11, 16, 16, 16, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 4, 16, 16, 16, 16, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 255) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1) `ZINC000195285465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000195285465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000195285465 none Cn1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2n2ccnn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 17, 17, 9, 17, 17, 17, 29, 29, 29, 29, 9, 9, 9, 9, 9, 9, 5, 17, 17, 17, 17, 29, 29, 9] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000195285465 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000195285465 Building ZINC000354072210 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354072210 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/256 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354072210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072210 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [45, 40, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 45, 45, 45, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/257 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/257' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354072210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072210 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [42, 39, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 42, 42, 42, 39, 39, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354072210 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 Building ZINC000354072210 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354072210 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 256) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072210.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354072210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072210 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [45, 40, 16, 16, 16, 16, 8, 1, 8, 1, 1, 1, 4, 4, 4, 4, 4, 16, 16, 16, 45, 45, 45, 40, 40, 16, 16, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 257) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072210.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354072210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072210 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [42, 39, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 15, 42, 42, 42, 39, 39, 15, 15, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354072210 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072210 Building ZINC000354072211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354072211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/258 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354072211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072211 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 35, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 41, 41, 41, 35, 35, 14, 14, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/259 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/259' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354072211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072211 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [44, 39, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 16, 44, 44, 44, 39, 39, 16, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354072211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 Building ZINC000354072211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354072211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 258) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/258: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354072211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072211 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 35, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 14, 14, 14, 41, 41, 41, 35, 35, 14, 14, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 259) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000354072211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354072211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000354072211 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [44, 39, 16, 16, 16, 16, 7, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 16, 16, 16, 44, 44, 44, 39, 39, 16, 16, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 151 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354072211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354072211 Building ZINC001088282729 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001088282729 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/260 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)C1) `ZINC001088282729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001088282729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001088282729 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)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', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 5, 12, 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, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 12, 16, 16, 16, 16, 16, 16, 16, 16, 33, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 50, 50, 50, 50, 150, 16, 16] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/261 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)C1) `ZINC001088282729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001088282729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001088282729 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)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', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 5, 12, 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, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 34, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 34, 50, 50, 50, 50, 150, 13, 13] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 329 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001088282729 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 Building ZINC001088282729 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001088282729 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 260) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)C1) `ZINC001088282729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001088282729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001088282729 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)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', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 5, 12, 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, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 12, 16, 16, 16, 16, 16, 16, 16, 16, 33, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 33, 50, 50, 50, 50, 150, 16, 16] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 321 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 261) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/261: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)C1) `ZINC001088282729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001088282729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001088282729 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCCCC[C@@H](NCCO)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', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 10, 5, 5, 12, 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, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 11, 13, 13, 13, 13, 13, 13, 13, 13, 34, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 34, 50, 50, 50, 50, 150, 13, 13] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 329 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001088282729 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001088282729 Building ZINC000354514645 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354514645 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/262 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000354514645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354514645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514645 none CN(C[C@@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 32, 42, 42, 42, 42, 42, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 23, 23, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/263 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000354514645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354514645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514645 none CN(C[C@@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 28, 37, 37, 37, 37, 37, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 19, 19, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354514645 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 Building ZINC000354514645 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354514645 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 262) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C[C@@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000354514645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354514645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514645 none CN(C[C@@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 32, 42, 42, 42, 42, 42, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 23, 23, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 136 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 263) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C[C@@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000354514645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354514645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514645 none CN(C[C@@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 28, 37, 37, 37, 37, 37, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 8, 8, 8, 19, 19, 37, 37, 37, 37, 37, 37, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354514645 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514645 Building ZINC000354514646 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354514646 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/264 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000354514646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354514646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514646 none CN(C[C@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 26, 36, 36, 36, 36, 36, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 20, 20, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/265 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/265' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000354514646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354514646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514646 none CN(C[C@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 31, 42, 42, 42, 42, 42, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 23, 23, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354514646 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 Building ZINC000354514646 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000354514646 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 264) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C[C@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000354514646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000354514646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514646 none CN(C[C@H]1CCOC1)C(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 26, 36, 36, 36, 36, 36, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 20, 20, 36, 36, 36, 36, 36, 36, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 122 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 265) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C[C@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000354514646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000354514646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000354514646 none CN(C[C@H]1CCOC1)C(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 12, 5, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 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: [8, 4, 8, 31, 42, 42, 42, 42, 42, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 8, 8, 8, 23, 23, 42, 42, 42, 42, 42, 42, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000354514646 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000354514646 Building ZINC000523693934 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693934 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/266 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693934 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 30, 48, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 34, 34, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/267 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693934 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 50, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 35, 35, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523693934 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 Building ZINC000523693934 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693934 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 266) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693934 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 30, 48, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 48, 48, 48, 48, 34, 34, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 267) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693934 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 50, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 35, 35, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523693934 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693934 Building ZINC000523693935 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693935 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/268 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693935 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 50, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 35, 35, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/269 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693935 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 30, 48, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 48, 48, 48, 48, 34, 34, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523693935 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 Building ZINC000523693935 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000523693935 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 268) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693935.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000523693935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693935 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 29, 50, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 50, 50, 50, 50, 35, 35, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 269) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1) `ZINC000523693935.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000523693935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000523693935 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccc(C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 30, 48, 22, 5, 5, 1, 5, 1, 1, 1, 4, 4, 2, 2, 4, 4, 48, 48, 48, 48, 34, 34, 22, 22, 5, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000523693935 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000523693935 Building ZINC000355007186 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355007186 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/270 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000355007186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355007186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000355007186 none Cc1ncsc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/271 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncsc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000355007186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355007186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000355007186 none Cc1ncsc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355007186 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 Building ZINC000355007186 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355007186 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 270) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ncsc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000355007186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355007186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000355007186 none Cc1ncsc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 271) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ncsc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000355007186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355007186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000355007186 none Cc1ncsc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 14, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 13, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 36, 13, 13, 2, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355007186 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355007186 Building ZINC000355146374 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355146374 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/272 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355146374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146374 none COC[C@@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 44, 26, 15, 25, 26, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 45, 45, 45, 44, 44, 78, 18, 18, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 303 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/273 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/273' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355146374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146374 none COC[C@@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 47, 28, 15, 26, 28, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 47, 47, 84, 20, 20, 14, 14, 2, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 331 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355146374 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 Building ZINC000355146374 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355146374 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 272) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355146374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146374 none COC[C@@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 44, 26, 15, 25, 26, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 45, 45, 45, 44, 44, 78, 18, 18, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 303 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 273) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355146374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146374 none COC[C@@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 47, 28, 15, 26, 28, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 47, 47, 84, 20, 20, 14, 14, 2, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 331 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355146374 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146374 Building ZINC000355146375 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355146375 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/274 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355146375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146375 none COC[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 47, 29, 15, 27, 29, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 87, 20, 20, 14, 14, 2, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 329 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/275 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/275' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355146375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146375 none COC[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 28, 15, 27, 28, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 46, 46, 46, 46, 46, 84, 17, 17, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 311 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355146375 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 Building ZINC000355146375 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355146375 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 274) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146375.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355146375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146375 none COC[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens 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, 47, 29, 15, 27, 29, 14, 2, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 47, 47, 47, 47, 47, 87, 20, 20, 14, 14, 2, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 329 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 275) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000355146375.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355146375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000355146375 none COC[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 28, 15, 27, 28, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 46, 46, 46, 46, 46, 84, 17, 17, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 311 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355146375 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355146375 Building ZINC000355152581 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355152581 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/276 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl) `ZINC000355152581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355152581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000355152581 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 3, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/277 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl) `ZINC000355152581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355152581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000355152581 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 6, 6, 6, 16, 16, 16, 6, 6, 3, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355152581 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 Building ZINC000355152581 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000355152581 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 276) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl) `ZINC000355152581.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000355152581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000355152581 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 19, 19, 19, 19, 19, 19, 6, 6, 6, 14, 14, 14, 6, 6, 3, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 277) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl) `ZINC000355152581.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000355152581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000355152581 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CNC(=O)C2)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 1, 1, 16, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 6, 2, 6, 6, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 6, 6, 6, 16, 16, 16, 6, 6, 3, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000355152581 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000355152581 Building ZINC000457329250 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457329250 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/278 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000457329250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457329250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000457329250 none CCNC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 22, 22, 12, 22, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 22, 12, 12, 12, 12, 12, 12, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/279 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/279' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000457329250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457329250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000457329250 none CCNC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 22, 22, 12, 22, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 22, 12, 12, 12, 12, 12, 12, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000457329250 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 Building ZINC000457329250 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000457329250 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 278) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCNC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000457329250.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000457329250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000457329250 none CCNC(=O)C(C)(C)NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 22, 22, 12, 22, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 22, 12, 12, 12, 12, 12, 12, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 279) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCNC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000457329250.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000457329250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000457329250 none CCNC(=O)C(C)(C)NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', '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, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 22, 22, 12, 22, 4, 12, 12, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 44, 44, 44, 44, 44, 22, 12, 12, 12, 12, 12, 12, 4, 3, 3, 1, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000457329250 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000457329250 Building ZINC000759647234 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759647234 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/280 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1) `ZINC000759647234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759647234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000759647234 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 17, 17, 17, 17, 17, 5, 5, 15, 15, 15, 15, 15, 5, 2, 6, 6, 27, 17, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/281 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/281' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1) `ZINC000759647234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759647234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000759647234 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 20, 20, 20, 20, 20, 5, 5, 12, 12, 12, 12, 12, 5, 3, 7, 7, 33, 20, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000759647234 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 Building ZINC000759647234 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000759647234 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 280) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1) `ZINC000759647234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000759647234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000759647234 none CCn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 9, 9, 9, 17, 17, 17, 17, 17, 5, 5, 15, 15, 15, 15, 15, 5, 2, 6, 6, 27, 17, 17, 17, 17, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 281) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1) `ZINC000759647234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000759647234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000759647234 none CCn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](O)c2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 12, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 7, 11, 11, 11, 20, 20, 20, 20, 20, 5, 5, 12, 12, 12, 12, 12, 5, 3, 7, 7, 33, 20, 20, 20, 20, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000759647234 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000759647234 Building ZINC000356387379 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000356387379 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/282 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1) `ZINC000356387379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000356387379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000356387379 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 26, 13, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 4, 26, 26, 78, 20, 20, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 240 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/283 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/283' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1) `ZINC000356387379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000356387379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000356387379 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 27, 13, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 4, 27, 27, 81, 19, 19, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 234 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000356387379 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 Building ZINC000356387379 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000356387379 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 282) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1) `ZINC000356387379.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000356387379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000356387379 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 26, 13, 20, 20, 20, 20, 9, 9, 9, 9, 9, 9, 4, 26, 26, 78, 20, 20, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 240 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 283) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1) `ZINC000356387379.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000356387379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000356387379 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CC(F)(F)F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 13, 13, 27, 13, 19, 19, 19, 19, 9, 9, 9, 9, 9, 9, 4, 27, 27, 81, 19, 19, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 234 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000356387379 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000356387379 Building ZINC000487516360 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487516360 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/284 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487516360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516360 none COCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 28, 22, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 42, 42, 42, 28, 28, 22, 22, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/285 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/285' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487516360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516360 none COCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 27, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 46, 46, 46, 33, 33, 27, 27, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487516360 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 Building ZINC000487516360 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487516360 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 284) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516360.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487516360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516360 none COCC[C@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 28, 22, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 42, 42, 42, 28, 28, 22, 22, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 285) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516360.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487516360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516360 none COCC[C@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 27, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 46, 46, 46, 33, 33, 27, 27, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487516360 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516360 Building ZINC000487516361 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487516361 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/286 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487516361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516361 none COCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 27, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 46, 46, 46, 33, 33, 27, 27, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/287 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/287' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487516361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516361 none COCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 22, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 42, 42, 42, 29, 29, 22, 22, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487516361 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 Building ZINC000487516361 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487516361 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 286) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487516361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516361 none COCC[C@@]1(NC(=O)[C@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 33, 27, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 46, 46, 46, 33, 33, 27, 27, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 287) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1) `ZINC000487516361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487516361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000487516361 none COCC[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2cccn2C)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 5, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 29, 22, 17, 9, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 42, 42, 42, 29, 29, 22, 22, 5, 4, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487516361 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487516361 Building ZINC000445942308 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000445942308 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/288 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1) `ZINC000445942308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000445942308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000445942308 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 18, 25, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18, 25, 25, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/289 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1) `ZINC000445942308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000445942308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000445942308 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 18, 25, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18, 25, 25, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000445942308 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 Building ZINC000445942308 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000445942308 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 288) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1) `ZINC000445942308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000445942308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000445942308 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 18, 25, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18, 25, 25, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 289) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1) `ZINC000445942308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000445942308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000445942308 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCCc2ncn(C)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 5, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 18, 25, 48, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18, 25, 25, 48, 48, 48, 48, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000445942308 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000445942308 Building ZINC000428426115 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428426115 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/290 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428426115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426115 none CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 11, 15, 15, 15, 15, 11, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/291 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/291' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428426115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426115 none CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 12, 23, 23, 23, 23, 12, 12, 12, 12, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428426115 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 Building ZINC000428426115 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428426115 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 290) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428426115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426115 none CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 11, 11, 11, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 11, 15, 15, 15, 15, 11, 11, 11, 11, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 291) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428426115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426115 none CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 12, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 6, 12, 23, 23, 23, 23, 12, 12, 12, 12, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428426115 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426115 Building ZINC000428426116 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428426116 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/292 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428426116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426116 none CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 11, 18, 18, 18, 18, 11, 11, 11, 11, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/293 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428426116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426116 none CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428426116 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 Building ZINC000428426116 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428426116 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 292) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428426116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426116 none CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 11, 11, 11, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 15, 15, 15, 6, 11, 18, 18, 18, 18, 11, 11, 11, 11, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 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]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 293) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1) `ZINC000428426116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428426116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428426116 none CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 13, 13, 13, 6, 12, 26, 26, 26, 26, 12, 12, 12, 12, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 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]) total number of confs: 108 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428426116 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428426116 Building ZINC000357536433 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357536433 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/294 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1) `ZINC000357536433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357536433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000357536433 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 32, 42, 47, 47, 47, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 19, 19, 47, 47, 47, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/295 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/295' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1) `ZINC000357536433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357536433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000357536433 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 27, 40, 46, 46, 46, 40, 40, 40, 5, 5, 5, 5, 5, 5, 3, 17, 17, 46, 46, 46, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000357536433 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 Building ZINC000357536433 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357536433 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 294) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1) `ZINC000357536433.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357536433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000357536433 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 32, 42, 47, 47, 47, 42, 42, 42, 5, 5, 5, 5, 5, 5, 4, 19, 19, 47, 47, 47, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 295) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1) `ZINC000357536433.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357536433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000357536433 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NCC1(S(C)(=O)=O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.o2', 'C.3', 'O.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'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 5, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 27, 40, 46, 46, 46, 40, 40, 40, 5, 5, 5, 5, 5, 5, 3, 17, 17, 46, 46, 46, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000357536433 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357536433 Building ZINC000985586190 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000985586190 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/296 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC000985586190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000985586190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985586190 none CC(=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', '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'] dock atom type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 18, 2, 18, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/297 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/297' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC000985586190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000985586190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985586190 none CC(=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', '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'] dock atom type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 23, 41, 23, 23, 23, 23, 23, 16, 2, 16, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23, 23, 41, 41, 41, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 41 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000985586190 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 Building ZINC000985586190 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000985586190 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 296) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)N1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC000985586190.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000985586190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985586190 none CC(=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', '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'] dock atom type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 50, 27, 27, 27, 27, 27, 18, 2, 18, 1, 1, 1, 2, 2, 2, 27, 27, 27, 27, 27, 50, 50, 50, 27, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 155 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 297) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)N1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC[C@@H]2C1) `ZINC000985586190.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000985586190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985586190 none CC(=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', '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'] dock atom type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 23, 41, 23, 23, 23, 23, 23, 16, 2, 16, 1, 1, 1, 2, 2, 2, 23, 23, 23, 23, 23, 41, 41, 41, 23, 23, 23, 23, 2, 2, 2, 2, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23] 41 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000985586190 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985586190 Building ZINC000487519777 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487519777 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/298 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C) `ZINC000487519777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487519777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487519777 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 19, 19, 39, 19, 25, 25, 25, 8, 8, 8, 8, 8, 8, 7, 39, 39, 117, 25, 25, 25, 25, 25, 25, 25, 25, 25] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 329 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/299 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C) `ZINC000487519777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487519777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487519777 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 19, 19, 40, 19, 24, 24, 24, 7, 7, 7, 7, 7, 7, 6, 40, 40, 120, 24, 24, 24, 24, 24, 24, 24, 24, 24] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 326 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487519777 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 Building ZINC000487519777 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000487519777 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 298) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C) `ZINC000487519777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000487519777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487519777 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 8, 8, 1, 1, 1, 1, 7, 7, 7, 19, 19, 39, 19, 25, 25, 25, 8, 8, 8, 8, 8, 8, 7, 39, 39, 117, 25, 25, 25, 25, 25, 25, 25, 25, 25] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 329 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 299) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C) `ZINC000487519777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000487519777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000487519777 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)C(C)(C)C 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', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 19, 19, 40, 19, 24, 24, 24, 7, 7, 7, 7, 7, 7, 6, 40, 40, 120, 24, 24, 24, 24, 24, 24, 24, 24, 24] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 326 number of broken/clashed sets: 110 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000487519777 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000487519777 Building ZINC000357954474 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357954474 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/300 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1) `ZINC000357954474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357954474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000357954474 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 37, 37, 8, 8, 8, 8, 8, 8, 6, 13, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/301 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/301' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1) `ZINC000357954474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357954474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000357954474 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 35, 35, 8, 8, 8, 8, 8, 8, 5, 11, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000357954474 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 Building ZINC000357954474 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000357954474 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 300) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/300: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1) `ZINC000357954474.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000357954474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000357954474 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 37, 37, 8, 8, 8, 8, 8, 8, 6, 13, 37, 37, 37, 37, 37] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 101 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 301) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/301: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1) `ZINC000357954474.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000357954474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000357954474 none Cn1cccc1[C@]([O-])([SiH3])C(=O)Nc1nncn1C1CC1 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.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 1, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 35, 35, 8, 8, 8, 8, 8, 8, 5, 11, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 97 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000357954474 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000357954474 Building ZINC000889031546 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000889031546 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/302 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000889031546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031546 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 16, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 10, 12, 12, 23, 23, 23, 23, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/303 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000889031546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031546 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 10, 12, 12, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000889031546 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 Building ZINC000889031546 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000889031546 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 302) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000889031546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031546 none C[C@@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 16, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 10, 12, 12, 23, 23, 23, 23, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 303) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000889031546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031546 none C[C@@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 10, 12, 12, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000889031546 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031546 Building ZINC000889031547 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000889031547 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/304 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000889031547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031547 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 11, 12, 12, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/305 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/305' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000889031547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031547 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 16, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 10, 12, 12, 23, 23, 23, 23, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000889031547 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 Building ZINC000889031547 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000889031547 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 304) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031547.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000889031547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031547 none C[C@]1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 11, 1, 11, 1, 1, 1, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 11, 12, 12, 24, 24, 24, 24, 24] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 305) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O) `ZINC000889031547.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000889031547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000889031547 none C[C@]1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CCNC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 5, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 4, 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] 0 hydrogens 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, 16, 10, 1, 10, 1, 1, 1, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 23, 23, 10, 12, 12, 23, 23, 23, 23, 23] 50 rigid atoms, others: [3, 5, 6, 7] set([0, 1, 2, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000889031547 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000889031547 Building ZINC000428441441 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428441441 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/306 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1) `ZINC000428441441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428441441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428441441 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 10, 13, 15, 15, 15, 15, 15, 15, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/307 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1) `ZINC000428441441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428441441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428441441 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428441441 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 Building ZINC000428441441 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428441441 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 306) grep: /scratch/xiaobo/365617/xds-8058088.97/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(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1) `ZINC000428441441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428441441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428441441 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 10, 13, 15, 15, 15, 15, 15, 15, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 307) grep: /scratch/xiaobo/365617/xds-8058088.97/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(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1) `ZINC000428441441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428441441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000428441441 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N2CCCNCC2)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 12, 12, 6, 6, 1, 1, 1, 2, 11, 12, 17, 17, 17, 17, 17, 17, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [8, 6, 7] set([0, 1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428441441 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428441441 Building ZINC000524960143 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524960143 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/308 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)on1) `ZINC000524960143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524960143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000524960143 none CCc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 36, 36, 21, 14, 14, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/309 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/309' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)on1) `ZINC000524960143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524960143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000524960143 none CCc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 36, 36, 21, 14, 14, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000524960143 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 Building ZINC000524960143 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000524960143 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 308) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)on1) `ZINC000524960143.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000524960143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000524960143 none CCc1cc(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 36, 36, 21, 14, 14, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 309) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)on1) `ZINC000524960143.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000524960143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000524960143 none CCc1cc(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 21, 21, 21, 14, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 21, 21, 36, 36, 36, 36, 36, 21, 14, 14, 2, 5, 5, 5, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000524960143 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000524960143 Building ZINC000428445751 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428445751 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/310 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428445751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445751 none CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 15, 15, 6, 15, 15, 6, 14, 27, 27, 27, 27, 14, 14, 14, 14, 6, 15, 15, 6, 15, 15, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/311 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428445751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445751 none CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 4, 1, 7, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 19, 27, 27, 27, 27, 19, 19, 19, 19, 6, 9, 9, 6, 9, 9, 6, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428445751 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 Building ZINC000428445751 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428445751 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 310) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428445751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445751 none CN[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 14, 14, 14, 14, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 15, 15, 6, 15, 15, 6, 14, 27, 27, 27, 27, 14, 14, 14, 14, 6, 15, 15, 6, 15, 15, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 311) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428445751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445751 none CN[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 19, 19, 19, 19, 4, 1, 7, 1, 1, 1, 6, 6, 6, 6, 9, 9, 6, 9, 9, 6, 19, 27, 27, 27, 27, 19, 19, 19, 19, 6, 9, 9, 6, 9, 9, 6, 19, 19] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428445751 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445751 Building ZINC000428445752 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428445752 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/312 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428445752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445752 none CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 16, 31, 31, 31, 31, 16, 16, 16, 16, 6, 10, 10, 6, 10, 10, 6, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/313 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428445752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445752 none CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 12, 12, 7, 12, 12, 6, 14, 29, 29, 29, 29, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428445752 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 Building ZINC000428445752 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428445752 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 312) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428445752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445752 none CN[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 16, 16, 16, 16, 16, 6, 1, 6, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 16, 31, 31, 31, 31, 16, 16, 16, 16, 6, 10, 10, 6, 10, 10, 6, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 313) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1) `ZINC000428445752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428445752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000428445752 none CN[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(c3ccccc3)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 14, 14, 14, 14, 14, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 12, 12, 7, 12, 12, 6, 14, 29, 29, 29, 29, 14, 14, 14, 14, 6, 12, 12, 12, 12, 12, 6, 14, 14] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428445752 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428445752 Building ZINC001040126952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001040126952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/314 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/314' -> `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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/315 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/315' -> `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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/316 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/316' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/317 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/317' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001040126952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 Building ZINC001040126952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001040126952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 314) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 315) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 316) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 317) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001040126952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 Building ZINC001040126952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001040126952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 314) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 315) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 316) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 317) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001040126952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 Building ZINC001040126952 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001040126952 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 314) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 315) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 316) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/316: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 23, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 314 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 317) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/317: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh 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@]2(C1)CCCN(CCO)C2) `ZINC001040126952.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001040126952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001040126952 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@]2(C1)CCCN(CCO)C2 NO_LONG_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', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total 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, 8, 25, 25, 25, 24, 25, 25, 25, 25, 25, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 24, 25, 25, 25, 25, 25, 25, 25, 50, 50, 50, 50, 150, 25, 25] 150 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 319 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001040126952 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001040126952 Building ZINC000525373642 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525373642 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/318 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCC1) `ZINC000525373642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525373642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525373642 none CCOC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 41, 41, 31, 41, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 45, 45, 45, 45, 45, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/319 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCC1) `ZINC000525373642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525373642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525373642 none CCOC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 42, 31, 42, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 46, 46, 46, 46, 46, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525373642 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 Building ZINC000525373642 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525373642 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 318) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCC1) `ZINC000525373642.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525373642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525373642 none CCOC(=O)C1(CNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 41, 41, 31, 41, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 45, 45, 45, 45, 45, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 319) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCC1) `ZINC000525373642.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525373642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525373642 none CCOC(=O)C1(CNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 42, 42, 31, 42, 18, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 46, 46, 46, 46, 46, 14, 14, 2, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525373642 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525373642 Building ZINC001271875778 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271875778 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/320 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2) `ZINC001271875778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271875778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271875778 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 4 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/321 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2) `ZINC001271875778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271875778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271875778 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5] 5 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271875778 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 Building ZINC001271875778 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271875778 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 320) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2) `ZINC001271875778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271875778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271875778 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4] 4 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 321) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2) `ZINC001271875778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271875778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271875778 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5] 5 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271875778 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271875778 Building ZINC001271876434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/322 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/323 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/324 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/324' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/325 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/325' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 Building ZINC001271876434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 322) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 323) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 324) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 325) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 Building ZINC001271876434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 322) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 323) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 324) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 325) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 Building ZINC001271876434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 322) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/322: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 323) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/323: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 324) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 35, 35, 35, 35, 35, 35, 48, 50, 50, 50, 50, 50, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 48, 48, 50, 50, 35, 35] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 325) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]c2)C1) `ZINC001271876434.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271876434 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CCN2Cc2cn[nH]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', 'C.3', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 1, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 34, 34, 34, 34, 34, 34, 48, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 48, 48, 50, 50, 34, 34] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876434 Building ZINC001271876627 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876627 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/326 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/327 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/328 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/328' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/329 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/329' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876627 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 Building ZINC001271876627 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876627 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 326) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 327) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 328) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 329) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876627 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 Building ZINC001271876627 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876627 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 326) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 327) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 328) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 329) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876627 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 Building ZINC001271876627 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876627 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 326) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 327) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 328) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/328: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 20, 2, 20, 1, 1, 1, 2, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 2, 2, 2, 2, 2, 2, 28, 28, 28, 28] 28 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 329) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/329: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876627.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876627 none CN1CCO[C@@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 20, 2, 19, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876627 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876627 Building ZINC001271876629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/330 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/331 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/331' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/332 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/332' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/333 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/333' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 Building ZINC001271876629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 330) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 331) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 332) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 333) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 Building ZINC001271876629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 330) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 331) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 332) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 333) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 Building ZINC001271876629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 330) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 331) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 332) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 2, 26, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 31 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 333) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/333: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271876629.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001271876629 none CN1CCO[C@]2(CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 22, 2, 25, 1, 1, 1, 2, 2, 2, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 2, 2, 2, 2, 2, 32, 32, 32, 32] 32 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876629 Building ZINC001271876665 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876665 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/334 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/335 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/335' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/336 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/336' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/337 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/337' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876665 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 Building ZINC001271876665 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876665 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 334) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 335) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 336) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 337) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876665 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 Building ZINC001271876665 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876665 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 334) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 335) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 336) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 337) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876665 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 Building ZINC001271876665 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876665 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 334) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 335) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 336) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/336: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 24, 15, 15, 15, 15, 15, 15, 4, 1, 10, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 49, 49, 24, 24, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 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]) total number of confs: 139 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 337) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876665.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876665 none COCCOCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 45, 25, 16, 16, 16, 16, 16, 16, 4, 1, 8, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 49, 49, 25, 25, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 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]) total number of confs: 137 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876665 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876665 Building ZINC001271876177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/338 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/339 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/339' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/340 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/340' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/341 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/341' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 Building ZINC001271876177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 338) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 339) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 340) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 341) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 Building ZINC001271876177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 338) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 339) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 340) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 341) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 Building ZINC001271876177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271876177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 338) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 339) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 340) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 17, 17, 17, 17, 17, 17, 16, 10, 1, 8, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 341) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001271876177.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271876177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876177 none CN(C)CCN1C[C@@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 35, 17, 17, 17, 17, 17, 17, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 17, 17, 50, 50, 50, 50, 50, 50, 36, 36, 35, 35, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 188 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876177 Building ZINC001271876426 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271876426 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/342 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876426 none COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 24, 10, 7, 13, 7, 13, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 49, 49, 24, 24, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 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]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/343 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/343' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876426 none COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 26, 11, 7, 14, 7, 14, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 49, 49, 26, 26, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876426 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 Building ZINC001271876426 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271876426 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 342) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271876426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876426 none COCCOCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 24, 10, 7, 13, 7, 13, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 49, 49, 24, 24, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 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]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 343) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271876426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271876426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001271876426 none COCCOCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 26, 11, 7, 14, 7, 14, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 49, 49, 26, 26, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 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]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271876426 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271876426 Building ZINC001271877027 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877027 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/344 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271877027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271877027 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 17, 31, 17, 24, 46, 50, 50, 50, 50, 50, 31, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 46, 46, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 317 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/345 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/345' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271877027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271877027 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 18, 31, 18, 25, 50, 50, 50, 50, 50, 50, 31, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877027 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 Building ZINC001271877027 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877027 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 344) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271877027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271877027 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 17, 31, 17, 24, 46, 50, 50, 50, 50, 50, 31, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 46, 46, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 317 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 345) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)C2)C1) `ZINC001271877027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001271877027 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC2(CN(Cc3cn[nH]c3)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', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', '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, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 10, 5, 1, 1, 8, 8, 6, 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, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 31, 18, 31, 18, 25, 50, 50, 50, 50, 50, 50, 31, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 304 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877027 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877027 Building ZINC001271877032 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877032 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/346 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/347 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/347' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/348 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/348' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/349 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/349' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877032 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 Building ZINC001271877032 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877032 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 346) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 347) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 348) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 349) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877032 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 Building ZINC001271877032 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877032 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 346) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 347) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 348) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 349) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877032 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 Building ZINC001271877032 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877032 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 346) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 347) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 348) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/348: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 24, 24, 24, 24, 24, 24, 4, 1, 9, 1, 1, 1, 1, 1, 1, 24, 24, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 50 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]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 349) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/349: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001271877032.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877032 none CN(C)CCN1CCC2(CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 25, 25, 25, 25, 25, 24, 4, 1, 11, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50, 50, 50, 50, 39, 39, 39, 39, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25] 50 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877032 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877032 Building ZINC001271877055 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877055 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/350 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271877055 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 18, 18, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/351 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/351' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271877055 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 20, 20, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877055 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 Building ZINC001271877055 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877055 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 350) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271877055 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 32, 18, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 43, 18, 18, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 351) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001271877055 none COCCOCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 36, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 44, 44, 20, 20, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 180 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877055 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877055 Building ZINC001271877069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/352 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877069 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 187 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/353 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/353' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877069 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 39, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 44, 44, 39, 39, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 Building ZINC001271877069 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877069 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 352) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877069 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 36, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 36, 36, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 187 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 353) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877069 none CN(C)CCN1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 39, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 44, 44, 39, 39, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 195 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877069 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877069 Building ZINC001271877078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/354 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/355 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/355' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/356 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/356' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/357 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/357' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 Building ZINC001271877078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 354) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 355) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 356) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 357) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 Building ZINC001271877078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 354) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 355) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 356) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 357) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 Building ZINC001271877078 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877078 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 354) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 355) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 356) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 50, 33, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 1, 10, 1, 1, 1, 2, 2, 2, 13, 50, 50, 50, 50, 50, 50, 36, 36, 33, 33, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 357) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/357: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877078.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001271877078 none CN(C)CCN1C[C@H]2C[C@@H](C1)N(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 38, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 2, 2, 2, 16, 50, 50, 50, 50, 50, 50, 42, 42, 38, 38, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877078 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877078 Building ZINC001271877394 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877394 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/358 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271877394 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 7 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/359 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/359' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271877394 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 31] 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]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877394 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 Building ZINC001271877394 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877394 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 358) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271877394 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 3, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2] 7 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 359) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001271877394 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 31] 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]) total number of confs: 9 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877394 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877394 Building ZINC001271877450 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877450 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/360 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/361 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/361' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/362 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/362' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/363 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/363' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877450 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 Building ZINC001271877450 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877450 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 360) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 361) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 362) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 363) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877450 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 Building ZINC001271877450 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877450 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 360) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 361) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 362) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 363) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877450 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 Building ZINC001271877450 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877450 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 360) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/360: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 361) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/361: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 362) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/362: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 50, 27, 20, 20, 20, 20, 20, 20, 4, 1, 9, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 28, 28, 27, 27, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 363) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877450.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877450 none CN(C)CCN1CCC12CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 28, 20, 20, 20, 20, 20, 20, 4, 1, 11, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 29, 29, 28, 28, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 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]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877450 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877450 Building ZINC001271877688 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877688 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/364 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001271877688 none CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 189 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/365 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/365' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001271877688 none CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 8, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 185 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877688 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 Building ZINC001271877688 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877688 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 364) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001271877688 none CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 9, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 189 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 365) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/365: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001271877688 none CN(C)CCN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 36, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 1, 8, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 37, 37, 36, 36, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 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]) total number of confs: 185 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877688 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877688 Building ZINC001271877836 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877836 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/366 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/367 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/367' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/368 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/368' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/369 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/369' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877836 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 Building ZINC001271877836 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877836 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 366) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 367) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 368) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 369) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877836 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 Building ZINC001271877836 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877836 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 366) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 367) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 368) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 369) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877836 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 Building ZINC001271877836 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271877836 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 366) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 367) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 368) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 50, 42, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 1, 15, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 43, 42, 42, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 181 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 369) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001271877836.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271877836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001271877836 none CN(C)CCN1CC[C@H]2[C@@H]1CCN2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 7, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 39, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 10, 1, 13, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 42, 39, 39, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 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]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877836 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877836 Building ZINC001271877888 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877888 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/370 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877888 none CN(C)CCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 37, 26, 19, 33, 19, 33, 22, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 39, 39, 37, 37, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 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]) total number of confs: 346 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/371 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/371' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877888 none CN(C)CCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 25, 18, 29, 18, 29, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 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]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877888 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 Building ZINC001271877888 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271877888 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 370) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271877888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877888 none CN(C)CCN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 37, 26, 19, 33, 19, 33, 22, 4, 1, 4, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 39, 39, 37, 37, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33] 50 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]) total number of confs: 346 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 371) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271877888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271877888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001271877888 none CN(C)CCN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 32, 25, 18, 29, 18, 29, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 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]) total number of confs: 301 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271877888 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271877888 Building ZINC001271879042 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271879042 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/372 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271879042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271879042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001271879042 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 20, 42, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 42, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/373 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/373' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271879042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271879042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001271879042 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 22, 44, 22, 22, 22, 22, 22, 4, 1, 8, 1, 1, 1, 3, 3, 3, 22, 50, 50, 50, 50, 50, 50, 50, 44, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271879042 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 Building ZINC001271879042 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271879042 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 372) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/372: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271879042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271879042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001271879042 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 20, 42, 20, 20, 20, 20, 20, 4, 1, 8, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 42, 20, 20, 20, 20, 20, 20, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 158 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 373) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/373: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2) `ZINC001271879042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271879042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001271879042 none CC(C)NC(=O)N1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 22, 44, 22, 22, 22, 22, 22, 4, 1, 8, 1, 1, 1, 3, 3, 3, 22, 50, 50, 50, 50, 50, 50, 50, 44, 22, 22, 22, 22, 22, 22, 3, 3, 3, 3, 3, 3, 3, 3, 3, 22, 22] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 156 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271879042 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271879042 Building ZINC000447079140 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447079140 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/374 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000447079140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447079140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079140 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 7, 7, 11, 21, 38, 44, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 7, 38, 38, 44, 44, 132, 21, 21, 21, 21, 21, 21] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 313 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/375 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/375' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000447079140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447079140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079140 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 6, 6, 11, 20, 38, 43, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 6, 38, 38, 43, 43, 129, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447079140 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 Building ZINC000447079140 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447079140 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 374) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000447079140.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447079140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079140 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 7, 7, 11, 21, 38, 44, 21, 21, 21, 21, 4, 4, 4, 4, 4, 4, 7, 38, 38, 44, 44, 132, 21, 21, 21, 21, 21, 21] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 313 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 375) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1) `ZINC000447079140.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447079140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079140 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 6, 6, 11, 20, 38, 43, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 6, 38, 38, 43, 43, 129, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447079140 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079140 Building ZINC000447079141 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447079141 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/376 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000447079141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447079141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079141 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 6, 6, 11, 20, 38, 43, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 6, 38, 38, 43, 43, 129, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/377 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/377' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000447079141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447079141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079141 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 7, 7, 11, 22, 40, 46, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 7, 40, 40, 46, 46, 138, 22, 22, 22, 22, 22, 22] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 326 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447079141 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 Building ZINC000447079141 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447079141 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 376) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000447079141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447079141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079141 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 6, 6, 11, 20, 38, 43, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 6, 38, 38, 43, 43, 129, 20, 20, 20, 20, 20, 20] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 377) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1) `ZINC000447079141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447079141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447079141 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N[C@]1(CCO)CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 1 hydrogens 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, 7, 7, 11, 22, 40, 46, 22, 22, 22, 22, 4, 4, 4, 4, 4, 4, 7, 40, 40, 46, 46, 138, 22, 22, 22, 22, 22, 22] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 326 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447079141 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447079141 Building ZINC000428471737 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428471737 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/378 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCN)cn1) `ZINC000428471737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428471737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428471737 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCN)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 14, 17, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 15, 15, 17, 17, 17, 17, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/379 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCN)cn1) `ZINC000428471737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428471737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428471737 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCN)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 17, 19, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 11, 11, 17, 17, 19, 19, 19, 19, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428471737 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 Building ZINC000428471737 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428471737 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 378) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/378: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCN)cn1) `ZINC000428471737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428471737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428471737 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)NCCCN)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 13, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 14, 17, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 2, 10, 10, 15, 15, 17, 17, 17, 17, 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]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 379) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/379: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCN)cn1) `ZINC000428471737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428471737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000428471737 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)NCCCN)cn1 NO_LONG_NAME dock atom types: ['C.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.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 10, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 17, 19, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 2, 11, 11, 17, 17, 19, 19, 19, 19, 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]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428471737 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428471737 Building ZINC000525804112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/380 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/381 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/382 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/382' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/383 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/383' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 Building ZINC000525804112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 380) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 381) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 382) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 383) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 Building ZINC000525804112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 380) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 381) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 382) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 383) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 Building ZINC000525804112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 380) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 381) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/381: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 14, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 31, 31] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 382) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 383) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/383: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804112.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804112 none C[C@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 13, 10, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 2, 7, 7, 7, 7, 7, 32, 32] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804112 Building ZINC000525804113 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804113 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/384 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/385 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/385' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/386 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/386' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/387 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/387' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804113 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 Building ZINC000525804113 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804113 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 384) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 385) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 386) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 387) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804113 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 Building ZINC000525804113 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804113 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 384) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 385) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 386) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 387) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804113 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 Building ZINC000525804113 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525804113 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 384) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/384: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 385) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/385: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 12, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 7, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 9, 9, 2, 7, 7, 7, 7, 7, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 386) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 387) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/387: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1) `ZINC000525804113.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525804113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525804113 none C[C@@H]1CCN(CCNC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 13, 10, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 10, 2, 6, 6, 6, 6, 6, 30, 30] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525804113 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525804113 Building ZINC000525942901 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942901 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/388 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/389 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/389' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/390 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/390' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/391 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/391' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942901 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 Building ZINC000525942901 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942901 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 388) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 389) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 390) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 391) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942901 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 Building ZINC000525942901 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942901 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 388) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 389) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 390) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 391) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942901 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 Building ZINC000525942901 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942901 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 388) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 389) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 1, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 390) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/390: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 391) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/391: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942901.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942901 none C[C@@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942901 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942901 Building ZINC000525942902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/392 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/393 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/393' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/394 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/394' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/395 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/395' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 Building ZINC000525942902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 392) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 393) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 394) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 395) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 Building ZINC000525942902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 392) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 393) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 394) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 395) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 Building ZINC000525942902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000525942902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 392) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 393) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 15, 15, 3, 3, 3, 1, 3, 3, 50, 50, 50, 50] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 394) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 395) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/395: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1) `ZINC000525942902.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000525942902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000525942902 none C[C@H]1CN(CCNC(=O)[C@]([O-])([SiH3])c2ccccc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 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: [49, 49, 49, 49, 22, 14, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 49, 49, 49, 49, 49, 49, 49, 49, 22, 22, 14, 14, 3, 3, 3, 3, 3, 3, 49, 49, 49, 49] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525942902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525942902 Building ZINC000525965879 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965879 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/396 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965879 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 13, 44, 44, 13, 13, 13, 13, 3, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 1, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/397 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/397' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965879 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 12, 41, 41, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 12, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 3, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965879 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 Building ZINC000525965879 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965879 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 396) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965879 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 13, 44, 44, 13, 13, 13, 13, 3, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 1, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 397) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965879 none CNS(=O)(=O)[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 12, 41, 41, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 12, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 3, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965879 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965879 Building ZINC000525965880 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965880 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/398 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965880 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 12, 41, 41, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 12, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 3, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/399 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965880 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 13, 44, 44, 13, 13, 13, 13, 3, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965880 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 Building ZINC000525965880 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965880 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 398) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965880 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 12, 41, 41, 12, 12, 12, 12, 3, 1, 5, 1, 1, 1, 3, 3, 1, 3, 3, 12, 50, 50, 50, 50, 12, 12, 12, 12, 3, 3, 1, 3, 3, 12, 12] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 399) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1) `ZINC000525965880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000525965880 none CNS(=O)(=O)[C@H]1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 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, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 13, 44, 44, 13, 13, 13, 13, 3, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 13, 50, 50, 50, 50, 13, 13, 13, 13, 2, 2, 2, 2, 2, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965880 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965880 Building ZINC000525965723 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965723 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/400 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000525965723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525965723 none O=C(C1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 32, 49, 49, 20, 20, 20, 8, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/401 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/401' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000525965723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525965723 none O=C(C1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 49, 49, 22, 22, 22, 7, 2, 11, 1, 1, 1, 3, 3, 1, 3, 3, 22, 22, 49, 49, 49, 49, 49, 22, 22, 22, 22, 3, 3, 1, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965723 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 Building ZINC000525965723 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000525965723 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 400) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(C1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000525965723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000525965723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525965723 none O=C(C1CC1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 20, 32, 49, 49, 20, 20, 20, 8, 1, 11, 1, 1, 1, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 20, 20, 20, 20, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 401) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(C1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1) `ZINC000525965723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000525965723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000525965723 none O=C(C1CC1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 32, 49, 49, 22, 22, 22, 7, 2, 11, 1, 1, 1, 3, 3, 1, 3, 3, 22, 22, 49, 49, 49, 49, 49, 22, 22, 22, 22, 3, 3, 1, 3, 3, 22, 22, 22, 22] 50 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000525965723 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000525965723 Building ZINC000447642243 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447642243 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/402 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1) `ZINC000447642243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447642243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000447642243 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 8, 13, 13, 17, 21, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 17, 17, 21, 21, 63, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/403 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/403' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1) `ZINC000447642243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447642243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000447642243 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 8, 13, 13, 18, 22, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 18, 18, 22, 22, 66, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447642243 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 Building ZINC000447642243 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447642243 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 402) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/402: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1) `ZINC000447642243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447642243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000447642243 none CCn1cc([C@@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 8, 13, 13, 17, 21, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 17, 17, 21, 21, 63, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 403) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/403: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1) `ZINC000447642243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447642243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000447642243 none CCn1cc([C@]([O-])([SiH3])C(=O)N(C)CCCCCO)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [9, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 8, 13, 13, 18, 22, 3, 3, 9, 9, 9, 9, 9, 3, 3, 3, 3, 8, 8, 13, 13, 13, 13, 18, 18, 22, 22, 66, 3] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447642243 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447642243 Building ZINC000447649076 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447649076 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/404 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCCCO) `ZINC000447649076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447649076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000447649076 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 12, 20, 25, 36, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 12, 12, 20, 20, 25, 25, 36, 36, 39, 39, 117] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 309 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/405 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/405' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCCCO) `ZINC000447649076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447649076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000447649076 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 13, 21, 27, 37, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 21, 21, 27, 27, 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]) total number of confs: 327 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447649076 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 Building ZINC000447649076 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447649076 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 404) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCCCO) `ZINC000447649076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447649076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000447649076 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 12, 20, 25, 36, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 12, 12, 20, 20, 25, 25, 36, 36, 39, 39, 117] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 309 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 405) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCCCO) `ZINC000447649076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447649076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000447649076 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCCCO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 5, 5, 13, 21, 27, 37, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 21, 21, 27, 27, 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]) total number of confs: 327 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447649076 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447649076 Building ZINC000447743570 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743570 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/406 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000447743570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743570 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 21, 21, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/407 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000447743570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743570 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 32, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 19, 19, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743570 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 Building ZINC000447743570 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743570 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 406) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000447743570.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743570 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 21, 21, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 297 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 407) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/407: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C) `ZINC000447743570.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743570 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 32, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 19, 19, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 295 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743570 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743570 Building ZINC000447743571 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743571 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/408 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000447743571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743571 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 23, 23, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/409 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/409' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000447743571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743571 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 21, 21, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 304 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743571 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 Building ZINC000447743571 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743571 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 408) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000447743571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743571 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 23, 23, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 305 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 409) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C) `ZINC000447743571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743571 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 21, 21, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 304 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743571 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743571 Building ZINC000447743572 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743572 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/410 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000447743572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743572 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 33, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 5, 25, 25, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/411 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/411' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000447743572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743572 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 5, 21, 21, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 286 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743572 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 Building ZINC000447743572 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743572 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 410) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000447743572.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743572 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 33, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 5, 25, 25, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 293 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 411) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C) `ZINC000447743572.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743572 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 34, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 5, 21, 21, 147, 49, 49, 49, 49, 49, 49, 49] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 286 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743572 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743572 Building ZINC000447743573 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743573 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/412 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000447743573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 307 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/413 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/413' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000447743573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 20, 20, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743573 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 Building ZINC000447743573 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447743573 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 412) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000447743573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447743573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743573 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 26, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 22, 22, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 307 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 413) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C) `ZINC000447743573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447743573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447743573 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)NC[C@]1(O)CCO[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 34, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 4, 20, 20, 150, 50, 50, 50, 50, 50, 50, 50] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 294 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447743573 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447743573 Building ZINC000447755587 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447755587 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/414 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1) `ZINC000447755587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447755587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755587 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/415 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/415' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1) `ZINC000447755587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447755587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755587 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 31, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447755587 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 Building ZINC000447755587 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447755587 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 414) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1) `ZINC000447755587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447755587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755587 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 415) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1) `ZINC000447755587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447755587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755587 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 31, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447755587 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755587 Building ZINC000447755589 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447755589 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/416 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1) `ZINC000447755589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447755589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755589 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 31, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/417 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/417' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1) `ZINC000447755589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447755589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755589 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 28, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447755589 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 Building ZINC000447755589 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447755589 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 416) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/416: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1) `ZINC000447755589.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447755589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755589 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 31, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 417) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1) `ZINC000447755589.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447755589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000447755589 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 28, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447755589 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447755589 Building ZINC000526958017 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000526958017 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/418 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000526958017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000526958017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000526958017 none CN(CCN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 20, 29, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 8, 8, 8, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/419 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN1CCCC1=O)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000526958017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000526958017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000526958017 none CN(CCN1CCCC1=O)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 20, 29, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 8, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 3, 3, 1, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000526958017 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 Building ZINC000526958017 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000526958017 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 418) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(CCN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000526958017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000526958017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000526958017 none CN(CCN1CCCC1=O)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 20, 29, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 2, 2, 1, 2, 2, 8, 8, 8, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 2, 2, 1, 2, 2] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 419) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(CCN1CCCC1=O)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000526958017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000526958017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000526958017 none CN(CCN1CCCC1=O)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 5, 5, 1, 11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 20, 29, 50, 50, 50, 50, 50, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 8, 8, 8, 20, 20, 29, 29, 50, 50, 50, 50, 50, 50, 3, 3, 1, 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]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000526958017 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000526958017 Building ZINC000447840972 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447840972 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/420 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000447840972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447840972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000447840972 none COCC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 35, 35, 35, 32, 32, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/421 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/421' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000447840972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447840972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000447840972 none COCC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 36, 36, 36, 33, 33, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447840972 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 Building ZINC000447840972 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447840972 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 420) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000447840972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447840972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000447840972 none COCC1(C)CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 16, 16, 16, 16, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 16, 35, 35, 35, 32, 32, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 421) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1) `ZINC000447840972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447840972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000447840972 none COCC1(C)CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 17, 17, 17, 17, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 17, 36, 36, 36, 33, 33, 17, 17, 17, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 17, 17] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447840972 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447840972 Building ZINC000447844778 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447844778 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/422 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1) `ZINC000447844778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447844778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000447844778 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [14, 4, 4, 4, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 23, 30, 12, 4, 4, 14, 14, 14, 14, 14, 4, 12, 12, 12, 12, 12, 23, 23, 30, 30, 30, 12, 12, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/423 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1) `ZINC000447844778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447844778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000447844778 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [14, 4, 4, 4, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 17, 22, 9, 4, 4, 14, 14, 14, 14, 14, 4, 9, 9, 9, 9, 9, 17, 17, 22, 22, 22, 9, 9, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447844778 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 Building ZINC000447844778 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000447844778 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 422) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1) `ZINC000447844778.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000447844778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000447844778 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [14, 4, 4, 4, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 23, 30, 12, 4, 4, 14, 14, 14, 14, 14, 4, 12, 12, 12, 12, 12, 23, 23, 30, 30, 30, 12, 12, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 423) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1) `ZINC000447844778.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000447844778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000447844778 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC(C)(COC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 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: [14, 4, 4, 4, 1, 1, 1, 1, 2, 2, 9, 9, 9, 9, 17, 22, 9, 4, 4, 14, 14, 14, 14, 14, 4, 9, 9, 9, 9, 9, 17, 17, 22, 22, 22, 9, 9, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000447844778 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000447844778 Building ZINC000527207254 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207254 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/424 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207254 none COC[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 27, 17, 30, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 47, 47, 47, 47, 45, 30, 30, 30, 90, 17, 17, 4, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/425 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/425' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207254 none COC[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 29, 17, 32, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 32, 32, 32, 96, 17, 17, 3, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 336 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207254 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 Building ZINC000527207254 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207254 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 424) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/424: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207254 none COC[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 27, 17, 30, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 47, 47, 47, 47, 45, 30, 30, 30, 90, 17, 17, 4, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 425) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/425: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207254 none COC[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 29, 17, 32, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 32, 32, 32, 96, 17, 17, 3, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 336 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207254 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207254 Building ZINC000527207255 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207255 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/426 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207255 none COC[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 29, 17, 32, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 32, 32, 32, 96, 17, 17, 3, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 336 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/427 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207255 none COC[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 27, 17, 30, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 47, 47, 47, 47, 45, 30, 30, 30, 90, 17, 17, 4, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207255 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 Building ZINC000527207255 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207255 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 426) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/426: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207255 none COC[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 29, 17, 32, 32, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 32, 32, 32, 96, 17, 17, 3, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 336 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 427) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/427: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000527207255 none COC[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 47, 27, 17, 30, 30, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 47, 47, 47, 47, 45, 30, 30, 30, 90, 17, 17, 4, 3, 3, 1, 3, 3] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 327 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207255 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207255 Building ZINC000527207282 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207282 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/428 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000527207282 none CN(C)CCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 30, 15, 4, 3, 4, 7, 9, 19, 19, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 30, 30, 30, 30, 30, 30, 19, 19, 15, 15, 7, 7, 9, 9, 19, 19, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/429 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/429' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000527207282 none CN(C)CCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 13, 3, 2, 3, 6, 8, 19, 19, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 31, 31, 31, 31, 31, 31, 17, 17, 13, 13, 6, 6, 8, 8, 19, 19, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207282 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 Building ZINC000527207282 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207282 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 428) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000527207282 none CN(C)CCN(CCN(C)C)C(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 19, 30, 15, 4, 3, 4, 7, 9, 19, 19, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 30, 30, 30, 30, 30, 30, 19, 19, 15, 15, 7, 7, 9, 9, 19, 19, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 186 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 429) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)CCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC000527207282 none CN(C)CCN(CCN(C)C)C(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 8, 5, 5, 10, 5, 5, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 13, 3, 2, 3, 6, 8, 19, 19, 1, 2, 1, 1, 1, 3, 3, 1, 3, 3, 31, 31, 31, 31, 31, 31, 17, 17, 13, 13, 6, 6, 8, 8, 19, 19, 19, 19, 19, 19, 3, 3, 1, 3, 3] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 188 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207282 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207282 Building ZINC000527207211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/430 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207211 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 48, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 34, 34, 21, 21, 5, 5, 5, 1, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/431 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/431' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207211 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 29, 46, 19, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 46, 46, 33, 33, 19, 19, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 Building ZINC000527207211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 430) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207211 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 48, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 34, 34, 21, 21, 5, 5, 5, 1, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 431) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207211 none CC1=NNC(=O)[C@@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 29, 46, 19, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 46, 46, 33, 33, 19, 19, 6, 4, 4, 4, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207211 Building ZINC000527207212 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207212 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/432 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207212 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 29, 46, 19, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 46, 46, 33, 33, 19, 19, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/433 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/433' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207212 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 48, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 34, 34, 21, 21, 5, 5, 5, 1, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207212 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 Building ZINC000527207212 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527207212 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 432) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527207212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527207212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207212 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 29, 46, 19, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 46, 46, 46, 46, 33, 33, 19, 19, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 433) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527207212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527207212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000527207212 none CC1=NNC(=O)[C@H]1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 26, 48, 21, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 48, 48, 48, 48, 34, 34, 21, 21, 5, 5, 5, 1, 5, 5] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527207212 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527207212 Building ZINC000527498089 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498089 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/434 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498089 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 29, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 29, 46, 46, 46, 29, 29, 29, 19, 19, 4, 5, 5, 1, 5, 5, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/435 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/435' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498089 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 48, 48, 48, 29, 29, 29, 20, 20, 4, 3, 3, 1, 3, 3, 48, 48, 48] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498089 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 Building ZINC000527498089 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498089 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 434) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498089 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 19, 29, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 29, 46, 46, 46, 29, 29, 29, 19, 19, 4, 5, 5, 1, 5, 5, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 435) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/435: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498089 none C[C@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 29, 48, 48, 48, 29, 29, 29, 20, 20, 4, 3, 3, 1, 3, 3, 48, 48, 48] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 226 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498089 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498089 Building ZINC000527498090 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498090 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/436 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498090 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 28, 28, 28, 19, 19, 4, 3, 3, 1, 3, 3, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/437 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/437' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498090 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 28, 46, 46, 46, 28, 28, 28, 19, 19, 4, 5, 5, 1, 5, 5, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498090 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 Building ZINC000527498090 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498090 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 436) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498090 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 28, 47, 47, 47, 28, 28, 28, 19, 19, 4, 3, 3, 1, 3, 3, 47, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 437) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)S(C)(=O)=O) `ZINC000527498090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000527498090 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])c1ccccc1)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 14, 5, 11, 11, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 4, 4, 1, 4, 1, 1, 1, 5, 5, 1, 5, 5, 28, 46, 46, 46, 28, 28, 28, 19, 19, 4, 5, 5, 1, 5, 5, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 215 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498090 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498090 Building ZINC000527498123 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498123 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/438 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527498123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000527498123 none Cn1cncc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 29, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 29, 29, 19, 19, 5, 5, 5, 1, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/439 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/439' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527498123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000527498123 none Cn1cncc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 29, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 29, 29, 19, 19, 5, 5, 5, 1, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498123 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 Building ZINC000527498123 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527498123 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 438) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cncc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527498123.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527498123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000527498123 none Cn1cncc1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 29, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 29, 29, 19, 19, 5, 5, 5, 1, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 439) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cncc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527498123.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527498123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000527498123 none Cn1cncc1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 29, 19, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 45, 45, 45, 45, 45, 29, 29, 19, 19, 5, 5, 5, 1, 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]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527498123 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527498123 Building ZINC000527497977 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527497977 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/440 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nncn1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527497977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527497977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000527497977 none CCc1nncn1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 28, 16, 16, 13, 13, 3, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/441 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nncn1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527497977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527497977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000527497977 none CCc1nncn1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 28, 16, 16, 13, 13, 3, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527497977 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 Building ZINC000527497977 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000527497977 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 440) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCc1nncn1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000527497977.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000527497977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000527497977 none CCc1nncn1CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 28, 16, 16, 13, 13, 3, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 441) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCc1nncn1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC000527497977.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000527497977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000527497977 none CCc1nncn1CCNC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', '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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 28, 28, 28, 28, 28, 16, 13, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 48, 48, 48, 48, 48, 28, 16, 16, 13, 13, 3, 3, 3, 1, 3, 3] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000527497977 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000527497977 Building ZINC000448601295 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000448601295 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/442 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000448601295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000448601295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000448601295 none O=C(NCCN1CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 20, 36, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/443 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/443' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000448601295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000448601295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000448601295 none O=C(NCCN1CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 20, 37, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000448601295 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 Building ZINC000448601295 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000448601295 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 442) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/442: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000448601295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000448601295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000448601295 none O=C(NCCN1CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 20, 36, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 30, 30, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 443) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/443: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCN1CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000448601295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000448601295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000448601295 none O=C(NCCN1CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 4, 4, 20, 37, 49, 49, 49, 49, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 20, 20, 31, 31, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3, 6, 3, 3] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000448601295 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000448601295 Building ZINC001271968882 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271968882 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/444 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C12CC(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2) `ZINC001271968882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271968882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001271968882 none NC(=O)C12CC(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 26, 9, 9, 7, 7, 1, 7, 1, 1, 1, 9, 11, 11, 9, 11, 11, 11, 9, 9, 26, 26, 9, 9, 7, 9, 9, 11, 11, 22, 11, 11, 9, 9, 9, 9] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/445 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C12CC(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2) `ZINC001271968882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271968882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001271968882 none NC(=O)C12CC(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 15, 15, 7, 7, 1, 7, 1, 1, 1, 9, 11, 11, 9, 11, 11, 11, 15, 15, 26, 26, 15, 15, 7, 9, 9, 11, 11, 22, 11, 11, 15, 15, 15, 15] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271968882 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 Building ZINC001271968882 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271968882 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 444) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)C12CC(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2) `ZINC001271968882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271968882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001271968882 none NC(=O)C12CC(NC(=O)[C@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 9, 26, 9, 9, 7, 7, 1, 7, 1, 1, 1, 9, 11, 11, 9, 11, 11, 11, 9, 9, 26, 26, 9, 9, 7, 9, 9, 11, 11, 22, 11, 11, 9, 9, 9, 9] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 445) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)C12CC(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2) `ZINC001271968882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271968882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001271968882 none NC(=O)C12CC(NC(=O)[C@@]([O-])([SiH3])Cc3ccc(O)cc3)(C1)C2 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 1, 5, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [26, 15, 26, 15, 15, 7, 7, 1, 7, 1, 1, 1, 9, 11, 11, 9, 11, 11, 11, 15, 15, 26, 26, 15, 15, 7, 9, 9, 11, 11, 22, 11, 11, 15, 15, 15, 15] 100 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271968882 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271968882 Building ZINC000340127196 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340127196 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/446 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1) `ZINC000340127196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340127196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000340127196 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 5, 5, 5, 1, 1, 1, 2, 6, 10, 13, 13, 13, 13, 13, 13, 5, 5, 19, 19, 19, 19, 19, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/447 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/447' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1) `ZINC000340127196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340127196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000340127196 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 5, 5, 5, 1, 1, 1, 2, 5, 10, 13, 13, 13, 13, 13, 13, 5, 5, 21, 21, 21, 21, 21, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340127196 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 Building ZINC000340127196 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340127196 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 446) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/446: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1) `ZINC000340127196.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340127196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000340127196 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 5, 5, 5, 1, 1, 1, 2, 6, 10, 13, 13, 13, 13, 13, 13, 5, 5, 19, 19, 19, 19, 19, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 447) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/447: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1) `ZINC000340127196.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340127196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000340127196 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCCOCC2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 5, 5, 5, 1, 1, 1, 2, 5, 10, 13, 13, 13, 13, 13, 13, 5, 5, 21, 21, 21, 21, 21, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340127196 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340127196 Building ZINC001271980695 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271980695 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/448 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/449 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/450 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/450' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/451 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/451' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271980695 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 Building ZINC001271980695 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271980695 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 448) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 449) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 450) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 451) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271980695 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 Building ZINC001271980695 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271980695 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 448) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 449) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 450) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 451) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271980695 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 Building ZINC001271980695 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271980695 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 448) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 449) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 8, 8, 1, 1, 1, 1, 6, 6, 38, 38, 38, 38, 38, 38, 38, 8, 8, 8, 8, 8, 8, 8, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 450) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 451) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/451: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1) `ZINC001271980695.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271980695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271980695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CC3(CCN3C)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 7, 7, 1, 1, 1, 1, 6, 6, 40, 40, 40, 40, 40, 40, 40, 7, 7, 7, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 7, 7] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271980695 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271980695 Building ZINC000340148941 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148941 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/452 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148941 none CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 22, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 20, 6, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 13, 13, 8, 8, 8, 3, 6, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/453 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/453' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148941 none CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 18, 22, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 21, 6, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 11, 11, 7, 7, 7, 2, 6, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340148941 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 Building ZINC000340148941 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148941 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 452) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148941.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148941 none CCN(CC)C[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 17, 22, 8, 3, 8, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 20, 6, 19, 19, 19, 19, 19, 22, 22, 22, 22, 22, 13, 13, 8, 8, 8, 3, 6, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 179 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 453) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148941.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148941 none CCN(CC)C[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 11, 18, 22, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 21, 6, 20, 20, 20, 20, 20, 22, 22, 22, 22, 22, 11, 11, 7, 7, 7, 2, 6, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340148941 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148941 Building ZINC000340148942 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148942 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/454 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148942 none CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 11, 15, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 19, 6, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 11, 11, 7, 7, 7, 2, 6, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/455 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/455' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148942 none CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 11, 15, 17, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 20, 6, 22, 22, 22, 22, 22, 17, 17, 17, 17, 17, 11, 11, 7, 7, 7, 3, 6, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340148942 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 Building ZINC000340148942 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000340148942 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 454) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000340148942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148942 none CCN(CC)C[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 11, 15, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 19, 6, 21, 21, 21, 21, 21, 17, 17, 17, 17, 17, 11, 11, 7, 7, 7, 2, 6, 19, 19, 19, 19, 19, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 455) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000340148942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000340148942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000340148942 none CCN(CC)C[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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, 10, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 15, 11, 15, 17, 7, 3, 7, 7, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 20, 6, 22, 22, 22, 22, 22, 17, 17, 17, 17, 17, 11, 11, 7, 7, 7, 3, 6, 20, 20, 20, 20, 20, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000340148942 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000340148942 Building ZINC000449135309 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449135309 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/456 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449135309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135309 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 26, 29, 29, 26, 29, 12, 19, 19, 6, 6, 6, 6, 6, 6, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 57, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/457 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/457' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449135309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135309 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 23, 27, 27, 23, 27, 10, 20, 20, 6, 6, 6, 6, 6, 6, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 60, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 260 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449135309 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 Building ZINC000449135309 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449135309 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 456) grep: /scratch/xiaobo/365617/xds-8058088.97/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([C@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449135309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135309 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 26, 29, 29, 26, 29, 12, 19, 19, 6, 6, 6, 6, 6, 6, 3, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 57, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 242 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 457) grep: /scratch/xiaobo/365617/xds-8058088.97/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([C@@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449135309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135309 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 23, 27, 27, 23, 27, 10, 20, 20, 6, 6, 6, 6, 6, 6, 2, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 60, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 260 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449135309 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135309 Building ZINC000449135310 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449135310 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/458 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449135310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135310 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 25, 28, 28, 25, 28, 10, 18, 18, 6, 6, 6, 6, 6, 6, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 54, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/459 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449135310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135310 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 28, 28, 25, 28, 12, 19, 19, 6, 6, 6, 6, 6, 6, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 57, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449135310 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 Building ZINC000449135310 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449135310 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 458) grep: /scratch/xiaobo/365617/xds-8058088.97/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([C@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135310.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449135310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135310 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 10, 25, 28, 28, 25, 28, 10, 18, 18, 6, 6, 6, 6, 6, 6, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 54, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 459) grep: /scratch/xiaobo/365617/xds-8058088.97/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([C@@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1) `ZINC000449135310.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449135310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449135310 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CCC(C)(C)C)C(=O)O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 5, 5, 5, 1, 11, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 25, 28, 28, 25, 28, 12, 19, 19, 6, 6, 6, 6, 6, 6, 3, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 57, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 239 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449135310 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449135310 Building ZINC001271993112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271993112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/460 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271993112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993112 none CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/461 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/461' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271993112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993112 none CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 Building ZINC001271993112 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271993112 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 460) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271993112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993112 none CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 44 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 461) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271993112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993112 none CN1C[C@H]2C[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 1, 9, 1, 1, 1, 10, 10, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 10, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993112 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993112 Building ZINC001271993137 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271993137 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/462 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2) `ZINC001271993137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993137 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 11, 11, 11, 11] 29 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/463 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/463' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2) `ZINC001271993137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993137 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 10, 10, 10, 10] 25 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993137 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 Building ZINC001271993137 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271993137 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 462) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2) `ZINC001271993137.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993137 none CN1C[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8, 11, 11, 11, 11] 29 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 463) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2) `ZINC001271993137.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993137 none CN1C[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H](C1)O2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 10, 10, 10, 10] 25 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993137 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993137 Building ZINC001271993342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/464 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/465 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/465' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/466 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/466' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/467 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/467' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 Building ZINC001271993342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 464) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 465) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 466) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 467) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 Building ZINC001271993342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 464) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 465) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 466) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 467) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 Building ZINC001271993342 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993342 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 464) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/464: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 465) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 26, 26] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 466) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 467) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/467: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21) `ZINC001271993342.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993342 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 6, 1, 1, 1, 6, 6, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993342 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993342 Building ZINC001271993344 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993344 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/468 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/469 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/469' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/470 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/470' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/471 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/471' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993344 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 Building ZINC001271993344 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993344 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 468) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 469) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 470) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 471) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993344 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 Building ZINC001271993344 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993344 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 468) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 469) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 470) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 471) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993344 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 Building ZINC001271993344 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993344 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 468) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/468: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 469) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 470) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 471) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/471: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21) `ZINC001271993344.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271993344 none CN1CCO[C@H]2CN(C(=O)[C@]([O-])([SiH3])c3cccc(F)c3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 12, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 9, 9, 9, 9, 22, 22] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993344 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993344 Building ZINC001271993989 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993989 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/472 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/473 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/473' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/474 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/474' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/475 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/475' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993989 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 Building ZINC001271993989 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993989 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 472) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 473) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 474) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 475) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993989 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 Building ZINC001271993989 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993989 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 472) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 473) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 474) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 475) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993989 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 Building ZINC001271993989 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001271993989 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 472) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 473) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 11, 1, 1, 1, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 6, 6, 6, 6, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 474) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/474: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 475) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/475: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271993989.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001271993989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271993989 none CN1CCC12CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 4, 1, 10, 1, 1, 1, 6, 6, 6, 6, 6, 6, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271993989 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271993989 Building ZINC001271991961 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271991961 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/476 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271991961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271991961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271991961 none CN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 26, 24, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/477 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/477' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271991961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271991961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271991961 none CN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271991961 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 Building ZINC001271991961 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271991961 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 476) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271991961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271991961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271991961 none CN1CC2(C1)CN(C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 25, 26, 24, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 477) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2) `ZINC001271991961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271991961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC001271991961 none CN1CC2(C1)CN(C(=O)[C@]([O-])([SiH3])c1cccc(F)c1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 10, 22, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271991961 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271991961 Building ZINC001271992586 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271992586 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/478 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271992586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271992586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271992586 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 41 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/479 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/479' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271992586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271992586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271992586 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 41 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271992586 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 Building ZINC001271992586 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001271992586 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 478) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271992586.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001271992586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271992586 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 41 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 479) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1) `ZINC001271992586.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001271992586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001271992586 none CN1C[C@@H]2COC[C@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cccc(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 8] 41 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001271992586 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001271992586 Building ZINC000119222681 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119222681 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/480 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1) `ZINC000119222681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119222681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222681 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 7, 10, 10, 19, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 33, 10, 10, 10, 10, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/481 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/481' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1) `ZINC000119222681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119222681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222681 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 7, 11, 11, 19, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 27, 11, 11, 11, 11, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119222681 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 Building ZINC000119222681 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119222681 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 480) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1) `ZINC000119222681.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119222681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222681 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 7, 10, 10, 19, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 33, 10, 10, 10, 10, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 481) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1) `ZINC000119222681.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119222681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222681 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 7, 11, 11, 19, 5, 5, 12, 12, 12, 12, 12, 5, 2, 9, 9, 27, 11, 11, 11, 11, 19, 19, 19, 5] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119222681 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222681 Building ZINC000119222772 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119222772 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/482 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1) `ZINC000119222772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119222772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222772 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 7, 11, 11, 21, 6, 6, 16, 16, 16, 16, 16, 6, 2, 9, 9, 27, 11, 11, 11, 11, 21, 21, 21, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/483 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1) `ZINC000119222772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119222772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222772 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 7, 10, 10, 19, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 33, 10, 10, 10, 10, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119222772 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 Building ZINC000119222772 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119222772 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 482) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1) `ZINC000119222772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119222772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222772 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 9, 7, 11, 11, 21, 6, 6, 16, 16, 16, 16, 16, 6, 2, 9, 9, 27, 11, 11, 11, 11, 21, 21, 21, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 483) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1) `ZINC000119222772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119222772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000119222772 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCSC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 14, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 7, 10, 10, 19, 6, 6, 14, 14, 14, 14, 14, 6, 2, 11, 11, 33, 10, 10, 10, 10, 19, 19, 19, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119222772 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119222772 Building ZINC000652912067 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912067 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/484 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912067 none O=C(N[C@@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 28, 14, 28, 35, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 28, 28, 84, 29, 29, 34, 35, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 311 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/485 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/485' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912067 none O=C(N[C@@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 32, 14, 31, 41, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 32, 32, 96, 33, 33, 41, 40, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912067 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 Building ZINC000652912067 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912067 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 484) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/484: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912067 none O=C(N[C@@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 28, 14, 28, 35, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 28, 28, 84, 29, 29, 34, 35, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 311 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 485) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/485: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912067 none O=C(N[C@@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 32, 14, 31, 41, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 32, 32, 96, 33, 33, 41, 40, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912067 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912067 Building ZINC000652912068 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912068 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/486 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912068 none O=C(N[C@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 33, 14, 31, 40, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 33, 33, 99, 33, 33, 39, 40, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/487 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912068 none O=C(N[C@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 15, 15, 30, 15, 30, 36, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 30, 30, 90, 31, 31, 36, 35, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 323 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912068 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 Building ZINC000652912068 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912068 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 486) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/486: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912068 none O=C(N[C@H](CO)CCF)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 14, 14, 33, 14, 31, 40, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 33, 33, 99, 33, 33, 39, 40, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 370 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 487) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/487: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N[C@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652912068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000652912068 none O=C(N[C@H](CO)CCF)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 12, 5, 5, 15, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [4, 1, 4, 4, 15, 15, 30, 15, 30, 36, 1, 1, 1, 3, 3, 1, 1, 3, 3, 4, 30, 30, 90, 31, 31, 36, 35, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 323 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912068 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912068 Building ZINC000449594042 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449594042 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/488 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449594042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594042 none C[C@@H](N)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 4, 13, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 23, 23, 23, 23, 23, 13, 13, 13, 4, 10, 17, 17, 10, 17, 17, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/489 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/489' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449594042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594042 none C[C@@H](N)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 4, 13, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 23, 23, 23, 23, 23, 13, 13, 13, 4, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449594042 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 Building ZINC000449594042 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449594042 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 488) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](N)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449594042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594042 none C[C@@H](N)[C@@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 4, 13, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 17, 17, 10, 17, 17, 10, 23, 23, 23, 23, 23, 13, 13, 13, 4, 10, 17, 17, 10, 17, 17, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 489) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](N)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449594042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594042 none C[C@@H](N)[C@@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 23, 23, 4, 13, 13, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 16, 16, 10, 16, 16, 10, 23, 23, 23, 23, 23, 13, 13, 13, 4, 10, 16, 16, 10, 16, 16, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449594042 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594042 Building ZINC000449594043 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449594043 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/490 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449594043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594043 none C[C@@H](N)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 24, 24, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 24, 24, 24, 24, 24, 11, 11, 11, 4, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/491 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/491' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449594043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594043 none C[C@@H](N)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 11, 26, 26, 4, 11, 11, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 26, 26, 26, 26, 26, 11, 11, 11, 4, 9, 12, 12, 12, 12, 12, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449594043 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 Building ZINC000449594043 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449594043 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 490) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/490: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449594043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594043 none C[C@@H](N)[C@H](C)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 11, 24, 24, 4, 11, 11, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 24, 24, 24, 24, 24, 11, 11, 11, 4, 10, 15, 15, 10, 15, 15, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 141 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 491) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/491: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](N)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449594043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449594043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449594043 none C[C@@H](N)[C@H](C)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 10, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 11, 26, 26, 4, 11, 11, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 12, 12, 9, 12, 12, 9, 26, 26, 26, 26, 26, 11, 11, 11, 4, 9, 12, 12, 12, 12, 12, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 145 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449594043 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449594043 Building ZINC000449607366 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449607366 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/492 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449607366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607366 none CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 18, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 22, 22, 22, 18, 18, 10, 10, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/493 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/493' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449607366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607366 none CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 9, 17, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 22, 22, 22, 22, 22, 17, 17, 9, 9, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449607366 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 Building ZINC000449607366 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449607366 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 492) grep: /scratch/xiaobo/365617/xds-8058088.97/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[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449607366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607366 none CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 18, 18, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 12, 12, 12, 6, 22, 22, 22, 22, 22, 18, 18, 10, 10, 3, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 136 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 493) grep: /scratch/xiaobo/365617/xds-8058088.97/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[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449607366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607366 none CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 17, 9, 17, 17, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 14, 14, 6, 22, 22, 22, 22, 22, 17, 17, 9, 9, 3, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 145 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449607366 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607366 Building ZINC000449607367 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449607367 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/494 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449607367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607367 none CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 23, 23, 23, 23, 23, 22, 22, 11, 11, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/495 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/495' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449607367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607367 none CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 21, 21, 21, 21, 21, 20, 20, 12, 12, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449607367 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 Building ZINC000449607367 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449607367 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 494) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607367.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449607367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607367 none CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 22, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 5, 23, 23, 23, 23, 23, 22, 22, 11, 11, 2, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 495) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000449607367.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449607367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449607367 none CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 19, 12, 20, 20, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 6, 21, 21, 21, 21, 21, 20, 20, 12, 12, 2, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449607367 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449607367 Building ZINC000449610409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449610409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/496 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449610409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610409 none CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 12, 31, 31, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 31, 32, 31, 31, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/497 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/497' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449610409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610409 none CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 13, 32, 32, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 32, 33, 32, 32, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449610409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 Building ZINC000449610409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449610409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 496) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/496: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449610409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610409 none CC[C@@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 29, 12, 31, 31, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 32, 32, 32, 31, 32, 31, 31, 12, 12, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 497) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/497: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449610409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610409 none CC[C@@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 31, 13, 32, 32, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 32, 33, 32, 32, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449610409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610409 Building ZINC000449610416 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449610416 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/498 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449610416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610416 none CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 16, 30, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 35, 35, 35, 35, 33, 30, 30, 16, 16, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/499 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/499' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449610416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610416 none CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 14, 26, 26, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 32, 32, 32, 32, 30, 26, 26, 14, 14, 3, 7, 8, 8, 8, 8, 8, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449610416 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 Building ZINC000449610416 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449610416 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 498) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/498: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449610416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610416 none CC[C@H](N)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 28, 16, 30, 30, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 35, 35, 35, 35, 33, 30, 30, 16, 16, 4, 7, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 167 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 499) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/499: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000449610416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449610416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000449610416 none CC[C@H](N)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 10, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 14, 26, 26, 3, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 8, 8, 7, 8, 8, 7, 32, 32, 32, 32, 30, 26, 26, 14, 14, 3, 7, 8, 8, 8, 8, 8, 7] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449610416 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449610416 Building ZINC000449631320 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449631320 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/500 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/501 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/501' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 18, 18, 18, 18, 18, 18, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/502 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/502' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/503 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/503' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 19, 19, 19, 19, 19, 19, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449631320 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 Building ZINC000449631320 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449631320 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 500) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 501) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 18, 18, 18, 18, 18, 18, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 502) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 503) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 19, 19, 19, 19, 19, 19, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449631320 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 Building ZINC000449631320 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449631320 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 500) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 501) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 18, 18, 18, 18, 18, 18, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 502) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 503) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 19, 19, 19, 19, 19, 19, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449631320 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 Building ZINC000449631320 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449631320 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 500) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 17, 17, 17, 17, 17, 17, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 81 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 501) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1) `ZINC000449631320.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 18, 18, 18, 18, 18, 18, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 502) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/502: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 10, 10, 4, 7, 16, 16, 16, 16, 16, 16, 7, 7, 7, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 79 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 503) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/503: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1) `ZINC000449631320.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449631320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000449631320 none CN(C(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1)[C@H]1C[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 7, 5, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 11, 11, 11, 4, 8, 19, 19, 19, 19, 19, 19, 8, 8, 8, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [2, 4, 5, 6] set([0, 1, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449631320 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449631320 Building ZINC000652912441 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912441 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/504 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652912441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912441 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 37, 16, 35, 41, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 37, 37, 39, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 400 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/505 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/505' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652912441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912441 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 38, 20, 35, 41, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912441 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 Building ZINC000652912441 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912441 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 504) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652912441.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912441 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 37, 16, 35, 41, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 37, 37, 39, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 400 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 505) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652912441.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912441 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 38, 20, 35, 41, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912441 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912441 Building ZINC000652912442 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912442 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/506 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652912442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912442 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 38, 20, 35, 41, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/507 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/507' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652912442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912442 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 37, 16, 35, 41, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 37, 37, 39, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 400 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912442 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 Building ZINC000652912442 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652912442 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 506) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652912442.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652912442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912442 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 20, 20, 38, 20, 35, 41, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 395 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 507) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652912442.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652912442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000652912442 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 16, 37, 16, 35, 41, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 37, 37, 39, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 400 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652912442 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652912442 Building ZINC000449694565 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694565 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/508 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/509 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/509' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/510 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/510' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/511 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/511' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694565 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 Building ZINC000449694565 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694565 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 508) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 509) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 510) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 511) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694565 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 Building ZINC000449694565 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694565 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 508) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 509) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 510) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 511) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694565 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 Building ZINC000449694565 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694565 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 508) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 509) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 510) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/510: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 1, 1, 1, 1, 5, 5, 5, 36, 44, 44, 44, 44, 44, 44, 44, 4, 4, 4, 4, 4, 4, 4, 5, 27, 27, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 143 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 511) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1) `ZINC000449694565.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694565 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 4, 4, 1, 1, 1, 1, 4, 4, 4, 35, 47, 47, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 4, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694565 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694565 Building ZINC000449694568 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694568 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/512 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/513 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/513' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/514 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/514' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/515 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/515' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694568 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 Building ZINC000449694568 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694568 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 512) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 513) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 514) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 515) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694568 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 Building ZINC000449694568 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694568 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 512) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 513) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 514) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 515) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694568 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 Building ZINC000449694568 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000449694568 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 512) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 513) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 514) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 33, 47, 47, 47, 47, 47, 47, 47, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 515) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1) `ZINC000449694568.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000449694568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000449694568 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCN2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 10, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 39, 45, 45, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 127 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449694568 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449694568 Building ZINC000449700308 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449700308 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/516 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1) `ZINC000449700308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449700308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700308 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/517 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/517' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1) `ZINC000449700308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449700308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700308 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449700308 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 Building ZINC000449700308 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449700308 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 516) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1) `ZINC000449700308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449700308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700308 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 19, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 517) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1) `ZINC000449700308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449700308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700308 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 25, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449700308 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700308 Building ZINC000449700309 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449700309 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/518 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1) `ZINC000449700309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449700309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700309 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 28, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/519 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/519' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1) `ZINC000449700309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449700309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700309 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449700309 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 Building ZINC000449700309 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000449700309 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 518) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/518: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1) `ZINC000449700309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000449700309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700309 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 28, 49, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 4, 21, 21, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 519) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/519: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1) `ZINC000449700309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000449700309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000449700309 none Cc1ccc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CNCCCO2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 10, 5, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 20, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000449700309 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000449700309 Building ZINC000150907420 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150907420 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/520 `/scratch/xiaobo/365617/xds-8058088.97/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)N(C)C[C@H](O)C1CC1) `ZINC000150907420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150907420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907420 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 16, 29, 29, 29, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 16, 16, 87, 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]) total number of confs: 248 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/521 `/scratch/xiaobo/365617/xds-8058088.97/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)N(C)C[C@H](O)C1CC1) `ZINC000150907420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150907420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907420 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 17, 28, 28, 28, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 17, 17, 84, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 256 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000150907420 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 Building ZINC000150907420 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150907420 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 520) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N(C)C[C@H](O)C1CC1) `ZINC000150907420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150907420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907420 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 16, 29, 29, 29, 39, 39, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 16, 16, 87, 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]) total number of confs: 248 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 521) grep: /scratch/xiaobo/365617/xds-8058088.97/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)N(C)C[C@H](O)C1CC1) `ZINC000150907420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150907420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907420 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 7, 7, 17, 28, 28, 28, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 7, 17, 17, 84, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 256 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000150907420 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907420 Building ZINC000150907462 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150907462 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/522 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1) `ZINC000150907462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150907462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907462 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 21, 27, 27, 27, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 21, 21, 81, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/523 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/523' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1) `ZINC000150907462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150907462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907462 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 20, 31, 31, 31, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 20, 20, 93, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 268 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000150907462 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 Building ZINC000150907462 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000150907462 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 522) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1) `ZINC000150907462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000150907462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907462 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 21, 27, 27, 27, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 21, 21, 81, 41, 41, 41, 41, 41] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 248 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 523) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1) `ZINC000150907462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000150907462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000150907462 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@@H](O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 8, 8, 20, 31, 31, 31, 42, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 20, 20, 93, 42, 42, 42, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 268 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000150907462 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000150907462 Building ZINC000119575330 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119575330 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/524 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000119575330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119575330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000119575330 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 16, 1, 1, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 39, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 14, 14, 39, 39, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/525 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/525' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000119575330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119575330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000119575330 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 16, 1, 1, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 44, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 14, 14, 44, 44, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119575330 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 Building ZINC000119575330 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000119575330 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 524) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000119575330.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000119575330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000119575330 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 16, 1, 1, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 39, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 14, 14, 39, 39, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 126 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 525) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC000119575330.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000119575330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC000119575330 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)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', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', '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, 16, 1, 1, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 44, 6, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 14, 14, 44, 44, 6, 6, 6, 6, 6, 14, 14, 14, 14] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 140 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000119575330 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000119575330 Building ZINC000928869209 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928869209 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/526 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928869209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869209 none CCN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 26, 26, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/527 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/527' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928869209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869209 none CCN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 29, 29, 29, 29, 29, 9, 29, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 29, 29, 43, 43, 43, 43, 43, 29, 29, 29, 29, 29, 29, 5, 5, 5, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928869209 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 Building ZINC000928869209 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928869209 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 526) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928869209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869209 none CCN1CCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 26, 26, 26, 26, 26, 12, 26, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 26, 26, 41, 41, 41, 41, 41, 26, 26, 26, 26, 26, 26, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 527) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928869209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869209 none CCN1CCC[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 29, 29, 29, 29, 29, 9, 29, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 29, 29, 43, 43, 43, 43, 43, 29, 29, 29, 29, 29, 29, 5, 5, 5, 1, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928869209 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869209 Building ZINC000928869211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928869211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/528 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928869211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869211 none CCN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 14, 30, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 30, 30, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 30, 5, 5, 5, 1, 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/529 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/529' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928869211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869211 none CCN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 13, 23, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 23, 23, 40, 40, 40, 40, 40, 23, 23, 23, 23, 23, 23, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928869211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 Building ZINC000928869211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928869211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 528) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928869211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869211 none CCN1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 14, 30, 5, 1, 5, 1, 1, 1, 5, 5, 1, 5, 5, 30, 30, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 30, 5, 5, 5, 1, 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]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 529) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O) `ZINC000928869211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928869211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928869211 none CCN1CCC[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 13, 23, 6, 1, 6, 1, 1, 1, 4, 4, 1, 4, 4, 23, 23, 40, 40, 40, 40, 40, 23, 23, 23, 23, 23, 23, 6, 4, 4, 1, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928869211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928869211 Building ZINC000985826410 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000985826410 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/530 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000985826410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000985826410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985826410 none CC(=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.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 29, 29, 29, 29, 29, 29, 14, 1, 19, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29, 50, 50, 50, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/531 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/531' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000985826410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000985826410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985826410 none CC(=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.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 50, 30, 30, 30, 30, 30, 30, 11, 1, 17, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] 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, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000985826410 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 Building ZINC000985826410 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000985826410 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 530) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/530: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000985826410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000985826410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985826410 none CC(=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.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 29, 29, 29, 29, 29, 29, 14, 1, 19, 1, 1, 1, 2, 2, 2, 29, 29, 29, 29, 50, 50, 50, 29, 29, 29, 29, 29, 29, 2, 2, 2, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 147 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 531) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/531: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@@H]2C1) `ZINC000985826410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000985826410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000985826410 none CC(=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.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'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 50, 30, 30, 30, 30, 30, 30, 11, 1, 17, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 12, 13, 14, 15, 16, 17, 31] 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, 40, 41, 42, 43]) total number of confs: 136 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000985826410 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000985826410 Building ZINC001019813034 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001019813034 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/532 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C1) `ZINC001019813034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001019813034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813034 none CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 35, 19, 19, 19, 19, 19, 19, 19, 19, 16, 2, 16, 1, 1, 1, 2, 2, 2, 19, 19, 19, 35, 35, 35, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19] 35 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: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/533 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/533' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C1) `ZINC001019813034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001019813034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813034 none CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 1, 1, 1, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 28 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001019813034 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 Building ZINC001019813034 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001019813034 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 532) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C1) `ZINC001019813034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001019813034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813034 none CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 19, 35, 19, 19, 19, 19, 19, 19, 19, 19, 16, 2, 16, 1, 1, 1, 2, 2, 2, 19, 19, 19, 35, 35, 35, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 19, 19] 35 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: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 533) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C1) `ZINC001019813034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001019813034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813034 none CC(=O)N1CC[C@@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 17, 28, 17, 17, 17, 17, 17, 17, 17, 17, 13, 2, 13, 1, 1, 1, 1, 1, 1, 17, 17, 17, 28, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 28 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 81 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001019813034 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813034 Building ZINC001019813035 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001019813035 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/534 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001019813035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001019813035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813035 none CC(=O)N1CC[C@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 24, 24, 24, 24, 24, 24, 24, 24, 17, 1, 17, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 36, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 36 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]) total number of confs: 95 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/535 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/535' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001019813035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001019813035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813035 none CC(=O)N1CC[C@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 39, 23, 23, 23, 23, 23, 23, 23, 23, 17, 1, 17, 1, 1, 1, 3, 3, 3, 23, 23, 23, 39, 39, 39, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23] 39 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 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: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001019813035 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 Building ZINC001019813035 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001019813035 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 534) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001019813035.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001019813035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813035 none CC(=O)N1CC[C@H]2OCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 24, 36, 24, 24, 24, 24, 24, 24, 24, 24, 17, 1, 17, 1, 1, 1, 1, 1, 1, 24, 24, 24, 36, 36, 36, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 36 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]) total number of confs: 95 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 535) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/535: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1) `ZINC001019813035.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001019813035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001019813035 none CC(=O)N1CC[C@H]2OCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 39, 23, 23, 23, 23, 23, 23, 23, 23, 17, 1, 17, 1, 1, 1, 3, 3, 3, 23, 23, 23, 39, 39, 39, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 3, 23, 23] 39 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 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: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001019813035 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001019813035 Building ZINC000120505931 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000120505931 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/536 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1) `ZINC000120505931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000120505931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000120505931 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 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: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 46, 46, 46, 46, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/537 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/537' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1) `ZINC000120505931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000120505931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000120505931 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 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: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000120505931 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 Building ZINC000120505931 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000120505931 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 536) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1) `ZINC000120505931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000120505931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000120505931 none Cc1ccc([C@@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 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: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 46, 46, 46, 46, 46, 46, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 46, 46, 46, 46, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 537) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1) `ZINC000120505931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000120505931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000120505931 none Cc1ccc([C@]([O-])([SiH3])C(=O)NCc2nccc(N)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 4, 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: [1, 1, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 49, 49, 49, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 49, 49, 49, 49, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000120505931 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000120505931 Building ZINC000428501580 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428501580 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/538 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428501580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428501580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC000428501580 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 16, 14, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 26, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 8, 8, 26, 26, 4, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/539 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428501580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428501580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC000428501580 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 16, 14, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 33, 6, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 10, 10, 33, 33, 6, 12, 12, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428501580 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 Building ZINC000428501580 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428501580 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 538) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/538: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428501580.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428501580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC000428501580 none NC(=O)C1(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 16, 14, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 8, 26, 4, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 8, 8, 26, 26, 4, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 539) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/539: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)CC1) `ZINC000428501580.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428501580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 29 natoms 28 natoms 27 natoms 26 names: ZINC000428501580 none NC(=O)C1(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'C.3', '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, 16, 14, 5, 5, 6, 6, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 33, 6, 6, 1, 6, 1, 1, 1, 12, 12, 12, 12, 12, 10, 10, 33, 33, 6, 12, 12, 10, 10, 10, 10] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428501580 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428501580 Building ZINC000529562073 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529562073 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/540 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000529562073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529562073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529562073 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 34, 15, 15, 3, 3, 3, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/541 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/541' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000529562073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529562073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529562073 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 34, 15, 15, 3, 3, 3, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529562073 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 Building ZINC000529562073 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529562073 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 540) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000529562073.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529562073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529562073 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 34, 15, 15, 3, 3, 3, 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]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 541) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000529562073.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529562073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529562073 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 34, 15, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 50, 50, 50, 50, 50, 34, 15, 15, 3, 3, 3, 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]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529562073 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562073 Building ZINC000529561722 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529561722 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/542 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000529561722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529561722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000529561722 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 31, 31, 31, 31, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 49, 49, 49, 49, 49, 31, 14, 14, 3, 2, 2, 2, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/543 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/543' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000529561722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529561722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000529561722 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 31, 31, 31, 31, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 49, 49, 49, 49, 49, 31, 14, 14, 3, 2, 2, 2, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529561722 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 Building ZINC000529561722 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529561722 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 542) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/542: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000529561722.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529561722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000529561722 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 31, 31, 31, 31, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 49, 49, 49, 49, 49, 31, 14, 14, 3, 2, 2, 2, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 543) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/543: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000529561722.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529561722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000529561722 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 31, 31, 31, 31, 31, 14, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 2, 49, 49, 49, 49, 49, 31, 14, 14, 3, 2, 2, 2, 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]) total number of confs: 183 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529561722 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529561722 Building ZINC000529562553 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529562553 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/544 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1) `ZINC000529562553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529562553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529562553 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 23, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 14, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/545 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/545' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1) `ZINC000529562553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529562553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529562553 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 14, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529562553 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 Building ZINC000529562553 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529562553 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 544) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1) `ZINC000529562553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529562553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529562553 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 23, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 14, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 545) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1) `ZINC000529562553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529562553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529562553 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cnnn2CC)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 8, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 14, 14, 14, 14, 21, 5, 5, 10, 10, 10, 10, 10, 5, 2, 9, 9, 14, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529562553 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529562553 Building ZINC000529556606 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529556606 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/546 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529556606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529556606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529556606 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 24, 11, 11, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/547 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/547' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529556606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529556606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529556606 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 24, 10, 10, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529556606 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 Building ZINC000529556606 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529556606 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 546) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/546: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529556606.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529556606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529556606 none CCn1nncc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 24, 11, 11, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 547) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/547: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000529556606.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529556606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529556606 none CCn1nncc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36, 24, 10, 10, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529556606 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529556606 Building ZINC000450398861 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450398861 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/548 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(CO)CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450398861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450398861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000450398861 none O=C(NC1(CO)CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 23, 39, 23, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 39, 39, 117, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/549 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/549' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(CO)CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450398861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450398861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000450398861 none O=C(NC1(CO)CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 23, 37, 23, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 37, 37, 111, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 272 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450398861 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 Building ZINC000450398861 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450398861 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 548) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC1(CO)CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450398861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450398861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000450398861 none O=C(NC1(CO)CCCC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 23, 39, 23, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 39, 39, 117, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 549) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC1(CO)CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450398861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450398861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000450398861 none O=C(NC1(CO)CCCC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 12, 23, 37, 23, 23, 23, 23, 1, 1, 1, 5, 5, 1, 1, 5, 5, 6, 37, 37, 111, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 10, 5, 5] 300 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 272 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450398861 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450398861 Building ZINC000450405774 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450405774 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/550 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450405774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405774 none CC[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 14, 5, 14, 14, 36, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 14, 14, 14, 36, 36, 108, 5, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 332 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/551 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/551' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450405774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405774 none CC[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 14, 6, 14, 14, 36, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 14, 14, 14, 36, 36, 108, 6, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450405774 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 Building ZINC000450405774 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450405774 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 550) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450405774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405774 none CC[C@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [24, 14, 5, 14, 14, 36, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 24, 24, 24, 24, 24, 14, 14, 14, 36, 36, 108, 5, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 332 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 551) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450405774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405774 none CC[C@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 14, 6, 14, 14, 36, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 14, 14, 14, 36, 36, 108, 6, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450405774 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405774 Building ZINC000450405775 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450405775 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/552 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450405775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405775 none CC[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 14, 6, 14, 14, 36, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 14, 14, 14, 36, 36, 108, 6, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/553 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/553' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450405775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405775 none CC[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 14, 5, 14, 14, 36, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 23, 23, 14, 14, 14, 36, 36, 108, 5, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 326 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450405775 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 Building ZINC000450405775 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000450405775 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 552) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000450405775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405775 none CC[C@@](C)(CO)NC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [26, 14, 6, 14, 14, 36, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 26, 26, 14, 14, 14, 36, 36, 108, 6, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 340 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 553) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000450405775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000450405775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000450405775 none CC[C@@](C)(CO)NC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 14, 5, 14, 14, 36, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 23, 23, 14, 14, 14, 36, 36, 108, 5, 5, 5, 10, 5, 5] 300 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 326 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000450405775 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000450405775 Building ZINC000529629653 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529629653 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/554 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529629653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529629653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529629653 none COCCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 17, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 34, 34, 34, 27, 27, 17, 17, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/555 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/555' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529629653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529629653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529629653 none COCCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 28, 28, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529629653 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 Building ZINC000529629653 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529629653 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 554) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529629653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529629653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529629653 none COCCC1CCN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 27, 17, 5, 5, 5, 5, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 5, 5, 34, 34, 34, 27, 27, 17, 17, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 555) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1) `ZINC000529629653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529629653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529629653 none COCCC1CCN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 12, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 18, 4, 4, 4, 4, 2, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 29, 29, 29, 28, 28, 18, 18, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529629653 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529629653 Building ZINC000302851259 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302851259 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/556 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/557 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/557' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/558 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/558' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/559 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/559' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302851259 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 Building ZINC000302851259 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302851259 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 556) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 557) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 558) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 559) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302851259 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 Building ZINC000302851259 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302851259 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 556) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 557) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 558) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 559) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302851259 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 Building ZINC000302851259 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000302851259 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 556) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 557) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1) `ZINC000302851259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 558) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/558: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 45, 45, 45, 45, 135, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 259 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 559) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/559: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1) `ZINC000302851259.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000302851259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000302851259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 18, 44, 44, 44, 44, 44, 44, 44, 44, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 44, 44, 44, 44, 132, 44, 44, 44, 44] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 254 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302851259 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302851259 Building ZINC000302892043 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302892043 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/560 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/560' -> `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)Nc1ncccc1O) `ZINC000302892043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302892043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000302892043 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 25, 25, 25, 50] 60 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/561 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/561' -> `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)Nc1ncccc1O) `ZINC000302892043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302892043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000302892043 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 25, 25, 25, 50] 60 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302892043 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 Building ZINC000302892043 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302892043 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 560) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1O) `ZINC000302892043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302892043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000302892043 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ncccc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 25, 25, 25, 50] 60 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 561) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1O) `ZINC000302892043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302892043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000302892043 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ncccc1O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 25, 25, 25, 50] 60 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 93 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000302892043 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000302892043 Building ZINC000888259452 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888259452 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/562 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000888259452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888259452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000888259452 none CCN(CCC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [6, 4, 3, 4, 10, 11, 25, 25, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 10, 10, 11, 11, 25, 25, 25, 25, 3, 3, 3, 3, 3, 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, 41, 42]) total number of confs: 101 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/563 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/563' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCC(=O)NC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000888259452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888259452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000888259452 none CCN(CCC(=O)NC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 3, 2, 3, 9, 10, 23, 23, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 10, 10, 23, 23, 23, 23, 2, 2, 2, 2, 2, 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, 41, 42]) total number of confs: 90 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888259452 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 Building ZINC000888259452 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888259452 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 562) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CCC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000888259452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888259452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000888259452 none CCN(CCC(=O)NC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [6, 4, 3, 4, 10, 11, 25, 25, 25, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 6, 6, 6, 6, 6, 10, 10, 11, 11, 25, 25, 25, 25, 3, 3, 3, 3, 3, 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, 41, 42]) total number of confs: 101 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 563) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CCC(=O)NC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000888259452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888259452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000888259452 none CCN(CCC(=O)NC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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: [4, 3, 2, 3, 9, 10, 23, 23, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 10, 10, 23, 23, 23, 23, 2, 2, 2, 2, 2, 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, 41, 42]) total number of confs: 90 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888259452 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888259452 Building ZINC000529691036 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529691036 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/564 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000529691036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529691036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529691036 none O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 38, 14, 14, 14, 40, 14, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 38, 38, 114, 40, 40, 120, 14, 14, 3, 3, 3, 3] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 472 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/565 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/565' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000529691036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529691036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529691036 none O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 8, 14, 14, 14, 14, 40, 14, 14, 14, 38, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 40, 40, 120, 38, 38, 114, 14, 14, 3, 3, 3, 3] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 474 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529691036 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 Building ZINC000529691036 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529691036 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 564) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000529691036.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529691036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529691036 none O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 38, 14, 14, 14, 40, 14, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 38, 38, 114, 40, 40, 120, 14, 14, 3, 3, 3, 3] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 472 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 565) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000529691036.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529691036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529691036 none O=C(N1C[C@@H](CO)[C@H](CO)C1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 8, 14, 14, 14, 14, 40, 14, 14, 14, 38, 14, 1, 1, 1, 3, 3, 1, 1, 3, 3, 14, 14, 40, 40, 120, 38, 38, 114, 14, 14, 3, 3, 3, 3] 450 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 474 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529691036 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529691036 Building ZINC000529692869 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529692869 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/566 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1) `ZINC000529692869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529692869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529692869 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 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: [1, 1, 3, 3, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 39, 14, 14, 14, 39, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 39, 39, 117, 39, 39, 117, 14, 14, 3, 3] 450 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 478 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/567 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/567' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1) `ZINC000529692869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529692869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529692869 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 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: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 39, 14, 14, 14, 38, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 39, 39, 117, 38, 38, 114, 14, 14, 3, 3] 450 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 471 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529692869 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 Building ZINC000529692869 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529692869 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 566) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1) `ZINC000529692869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529692869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529692869 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 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: [1, 1, 3, 3, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 39, 14, 14, 14, 39, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 39, 39, 117, 39, 39, 117, 14, 14, 3, 3] 450 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 478 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 567) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1) `ZINC000529692869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529692869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529692869 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2C[C@@H](CO)[C@H](CO)C2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 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: [1, 1, 3, 3, 1, 1, 1, 1, 4, 8, 14, 14, 14, 14, 39, 14, 14, 14, 38, 14, 3, 3, 3, 3, 3, 3, 3, 14, 14, 39, 39, 117, 38, 38, 114, 14, 14, 3, 3] 450 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 471 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529692869 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529692869 Building ZINC000529687809 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529687809 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/568 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC000529687809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529687809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529687809 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 44, 18, 18, 18, 42, 18, 3, 3, 3, 3, 3, 3, 18, 18, 44, 44, 132, 42, 42, 126, 18, 18] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 518 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/569 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/569' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC000529687809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529687809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529687809 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 8, 17, 17, 17, 17, 43, 17, 17, 17, 43, 17, 3, 3, 3, 3, 3, 3, 17, 17, 43, 43, 129, 43, 43, 129, 17, 17] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 529 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529687809 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 Building ZINC000529687809 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529687809 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 568) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC000529687809.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529687809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529687809 none Cc1ccc(F)cc1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 8, 18, 18, 18, 18, 44, 18, 18, 18, 42, 18, 3, 3, 3, 3, 3, 3, 18, 18, 44, 44, 132, 42, 42, 126, 18, 18] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 518 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 569) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1) `ZINC000529687809.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529687809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529687809 none Cc1ccc(F)cc1[C@]([O-])([SiH3])C(=O)N1C[C@@H](CO)[C@H](CO)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 7, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 8, 17, 17, 17, 17, 43, 17, 17, 17, 43, 17, 3, 3, 3, 3, 3, 3, 17, 17, 43, 43, 129, 43, 43, 129, 17, 17] 450 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 529 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529687809 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529687809 Building ZINC000928887947 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887947 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/570 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C) `ZINC000928887947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887947 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 38, 38, 38, 38, 38, 38, 38] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/571 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/571' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C) `ZINC000928887947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887947 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 18, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887947 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 Building ZINC000928887947 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887947 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 570) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C) `ZINC000928887947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887947 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 18, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 38, 38, 38, 38, 38, 38, 38] 48 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 571) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C) `ZINC000928887947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887947 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 10, 10, 18, 44, 44, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 44, 44, 44, 44, 44, 44, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 121 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887947 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887947 Building ZINC000928887963 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887963 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/572 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C) `ZINC000928887963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887963 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 15, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 31, 31, 31, 31, 31, 31, 31] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/573 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/573' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C) `ZINC000928887963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887963 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 37, 37, 37, 37] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887963 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 Building ZINC000928887963 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887963 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 572) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C) `ZINC000928887963.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887963 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 15, 31, 31, 31, 31, 31, 31, 31, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 31, 31, 31, 31, 31, 31, 31] 35 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 573) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C) `ZINC000928887963.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887963 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 37, 37, 37, 37] 46 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887963 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887963 Building ZINC000928887965 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887965 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/574 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C) `ZINC000928887965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 37, 37, 37, 37] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/575 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/575' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C) `ZINC000928887965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887965 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 Building ZINC000928887965 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887965 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 574) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C) `ZINC000928887965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887965 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 37, 37, 37, 37, 37, 37, 37, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 37, 37, 37, 37, 37, 37, 37] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 101 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 575) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C) `ZINC000928887965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887965 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 9, 9, 16, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 35, 35, 35, 35, 35, 35, 35] 43 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887965 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887965 Building ZINC000928887967 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887967 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/576 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C) `ZINC000928887967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887967 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 41, 41, 41, 41, 41, 41, 41] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/577 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/577' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C) `ZINC000928887967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887967 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 34, 34, 34, 34, 34, 34, 34] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887967 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 Building ZINC000928887967 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928887967 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 576) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C) `ZINC000928887967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928887967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887967 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 18, 41, 41, 41, 41, 41, 41, 41, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 41, 41, 41, 41, 41, 41, 41] 47 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 112 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 577) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C) `ZINC000928887967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928887967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000928887967 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1COC[C@@H]1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 16, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 34, 34, 34, 34, 34, 34, 34] 45 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 94 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928887967 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928887967 Building ZINC000529864272 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529864272 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/578 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000529864272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529864272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529864272 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [19, 18, 19, 12, 18, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/579 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/579' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000529864272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529864272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529864272 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 14, 26, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 3, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3] 29 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529864272 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 Building ZINC000529864272 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529864272 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 578) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000529864272.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529864272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529864272 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 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: [19, 18, 19, 12, 18, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 2, 2, 2, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2] 19 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 579) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000529864272.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529864272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000529864272 none CN(C)C(=O)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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, 5, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 14, 26, 14, 14, 14, 14, 14, 7, 1, 7, 1, 1, 1, 3, 3, 3, 26, 26, 26, 26, 26, 26, 14, 14, 14, 14, 14, 14, 3, 3, 3, 3, 3, 3, 3, 3, 3] 29 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 76 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529864272 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529864272 Building ZINC000529872270 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529872270 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/580 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC12CC(C1)CO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000529872270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529872270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529872270 none O=C(NCC12CC(C1)CO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/581 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/581' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC12CC(C1)CO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000529872270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529872270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529872270 none O=C(NCC12CC(C1)CO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 22, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 22, 22, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529872270 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 Building ZINC000529872270 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529872270 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 580) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCC12CC(C1)CO2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000529872270.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529872270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529872270 none O=C(NCC12CC(C1)CO2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 25, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 1, 4, 4, 5, 25, 25, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 137 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 581) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCC12CC(C1)CO2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000529872270.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529872270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000529872270 none O=C(NCC12CC(C1)CO2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 22, 45, 45, 45, 45, 45, 1, 1, 1, 4, 4, 1, 2, 4, 4, 4, 22, 22, 45, 45, 45, 45, 45, 45, 45, 4, 4, 8, 4, 4] 100 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529872270 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529872270 Building ZINC000529873751 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529873751 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/582 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1) `ZINC000529873751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529873751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529873751 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 23, 5, 5, 11, 11, 11, 11, 11, 5, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/583 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/583' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1) `ZINC000529873751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529873751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529873751 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 21, 21, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529873751 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 Building ZINC000529873751 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529873751 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 582) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1) `ZINC000529873751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529873751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529873751 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 13, 23, 23, 23, 23, 23, 5, 5, 11, 11, 11, 11, 11, 5, 2, 13, 13, 23, 23, 23, 23, 23, 23, 23, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 583) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1) `ZINC000529873751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529873751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000529873751 none CCn1cc([C@]([O-])([SiH3])C(=O)NCC23CC(C2)CO3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 10, 21, 21, 21, 21, 21, 5, 5, 13, 13, 13, 13, 13, 5, 2, 10, 10, 21, 21, 21, 21, 21, 21, 21, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529873751 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529873751 Building ZINC000529895561 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895561 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/584 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895561 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 36, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 49, 49, 49, 49, 49, 36, 36, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/585 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/585' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895561 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 34, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 50, 50, 50, 34, 34, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895561 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 Building ZINC000529895561 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895561 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 584) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/584: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895561 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 47, 36, 12, 12, 12, 12, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 49, 49, 49, 49, 49, 36, 36, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 585) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895561 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 47, 34, 12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 12, 12, 12, 50, 50, 50, 50, 50, 34, 34, 12, 12, 3, 3, 6, 3, 3, 12, 12, 12, 12] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 161 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895561 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895561 Building ZINC000529895562 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895562 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/586 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895562 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 37, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 50, 50, 50, 50, 50, 37, 37, 10, 10, 3, 3, 6, 3, 3, 10, 10, 10, 10] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/587 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/587' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895562 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 37, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 49, 49, 49, 49, 49, 37, 37, 13, 13, 3, 3, 6, 3, 3, 13, 13, 13, 13] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895562 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 Building ZINC000529895562 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895562 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 586) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895562 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [50, 49, 37, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 10, 10, 50, 50, 50, 50, 50, 37, 37, 10, 10, 3, 3, 6, 3, 3, 10, 10, 10, 10] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 587) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1) `ZINC000529895562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895562 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 37, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 3, 3, 1, 1, 3, 3, 13, 13, 13, 49, 49, 49, 49, 49, 37, 37, 13, 13, 3, 3, 6, 3, 3, 13, 13, 13, 13] 100 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 163 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895562 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895562 Building ZINC000529895016 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895016 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/588 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895016 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [48, 46, 32, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 48, 48, 48, 48, 48, 32, 32, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/589 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/589' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895016 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [44, 42, 28, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 9, 44, 44, 44, 44, 44, 28, 28, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895016 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 Building ZINC000529895016 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895016 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 588) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895016.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895016 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [48, 46, 32, 8, 8, 8, 8, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 48, 48, 48, 48, 48, 32, 32, 8, 8, 2, 2, 2, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 589) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895016.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895016 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [44, 42, 28, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 9, 44, 44, 44, 44, 44, 28, 28, 9, 9, 2, 2, 2, 2, 2, 2, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895016 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895016 Building ZINC000529895020 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895020 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/590 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895020 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [46, 45, 33, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 46, 46, 46, 46, 46, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/591 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/591' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895020 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 34, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 13, 47, 47, 47, 47, 47, 34, 34, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895020 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 Building ZINC000529895020 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529895020 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 590) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529895020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895020 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [46, 45, 33, 10, 10, 10, 10, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 46, 46, 46, 46, 46, 33, 33, 10, 10, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 591) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1) `ZINC000529895020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529895020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529895020 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cccn2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 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: [47, 47, 34, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 13, 13, 13, 47, 47, 47, 47, 47, 34, 34, 13, 13, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529895020 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529895020 Building ZINC000529897405 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529897405 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/592 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529897405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897405 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 13, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 6, 2, 4, 4, 4, 20, 20, 20, 20, 20, 13, 13, 4, 4, 2, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/593 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529897405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897405 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 13, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 11, 2, 5, 5, 5, 23, 23, 23, 23, 23, 13, 13, 5, 5, 2, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529897405 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 Building ZINC000529897405 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529897405 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 592) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529897405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897405 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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, 19, 13, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 6, 2, 4, 4, 4, 20, 20, 20, 20, 20, 13, 13, 4, 4, 2, 6, 6, 6, 6, 6, 2, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 593) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529897405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897405 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 13, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 2, 2, 2, 2, 11, 2, 5, 5, 5, 23, 23, 23, 23, 23, 13, 13, 5, 5, 2, 11, 11, 11, 11, 11, 2, 5, 5, 5, 5] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529897405 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897405 Building ZINC000529897406 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529897406 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/594 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529897406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897406 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 25, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 12, 3, 3, 3, 3, 26, 26, 26, 26, 26, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/595 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/595' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529897406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897406 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 13, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 3, 3, 3, 22, 22, 22, 22, 22, 13, 13, 3, 3, 4, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529897406 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 Building ZINC000529897406 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529897406 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 594) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529897406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897406 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 25, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 12, 3, 3, 3, 3, 26, 26, 26, 26, 26, 12, 12, 3, 3, 3, 12, 12, 12, 12, 12, 3, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 595) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1) `ZINC000529897406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529897406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529897406 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(CC)c2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 13, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 3, 3, 3, 22, 22, 22, 22, 22, 13, 13, 3, 3, 4, 10, 10, 10, 10, 10, 4, 3, 3, 3, 3] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529897406 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529897406 Building ZINC000529877659 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529877659 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/596 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2) `ZINC000529877659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529877659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529877659 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 20, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/597 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/597' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2) `ZINC000529877659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529877659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529877659 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529877659 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 Building ZINC000529877659 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529877659 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 596) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/596: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2) `ZINC000529877659.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529877659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529877659 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 20, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 597) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/597: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2) `ZINC000529877659.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529877659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000529877659 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC12CC(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 24, 49, 49, 49, 49, 49, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 24, 24, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529877659 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529877659 Building ZINC000529899363 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529899363 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/598 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529899363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899363 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 13, 13, 13, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 50, 36, 36, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/599 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/599' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529899363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899363 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 10, 10, 10, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529899363 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 Building ZINC000529899363 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529899363 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 598) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529899363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899363 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 36, 13, 13, 13, 13, 11, 1, 11, 1, 1, 1, 1, 1, 1, 13, 13, 13, 50, 50, 50, 50, 50, 36, 36, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 599) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529899363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899363 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 10, 10, 10, 10, 9, 1, 9, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 50, 50, 50, 50, 34, 34, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529899363 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899363 Building ZINC000529899366 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529899366 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/600 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529899366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899366 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/601 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/601' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529899366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899366 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 34, 34, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529899366 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 Building ZINC000529899366 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529899366 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 600) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529899366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899366 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 9, 9, 9, 9, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 50, 50, 50, 50, 50, 30, 30, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 601) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1) `ZINC000529899366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529899366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000529899366 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 34, 12, 12, 12, 12, 10, 1, 10, 1, 1, 1, 1, 1, 1, 12, 12, 12, 50, 50, 50, 50, 50, 34, 34, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12] 50 rigid atoms, others: [32, 33, 34, 35, 36, 8, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529899366 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529899366 Building ZINC000529933313 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529933313 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/602 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1) `ZINC000529933313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529933313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000529933313 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/603 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/603' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1) `ZINC000529933313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529933313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000529933313 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 6, 2, 9, 9, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529933313 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 Building ZINC000529933313 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529933313 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 602) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1) `ZINC000529933313.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529933313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000529933313 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 10, 14, 14, 14, 14, 14, 14, 6, 6, 15, 15, 15, 15, 15, 6, 2, 10, 10, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 603) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1) `ZINC000529933313.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529933313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000529933313 none CCn1cc([C@]([O-])([SiH3])C(=O)NCCc2cncnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 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: [15, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 9, 13, 13, 13, 13, 13, 13, 6, 6, 15, 15, 15, 15, 15, 6, 2, 9, 9, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529933313 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529933313 Building ZINC000529934646 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529934646 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/604 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/604' -> `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)NCCc1cncnc1) `ZINC000529934646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529934646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529934646 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cncnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 40, 44, 44, 35, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 25, 25, 40, 40, 44, 42, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 216 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/605 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/605' -> `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)NCCc1cncnc1) `ZINC000529934646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529934646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529934646 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cncnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 40, 44, 44, 35, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 25, 25, 40, 40, 44, 40, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529934646 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 Building ZINC000529934646 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529934646 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 604) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cncnc1) `ZINC000529934646.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529934646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529934646 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1cncnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 40, 44, 44, 35, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 25, 25, 40, 40, 44, 42, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 216 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 605) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cncnc1) `ZINC000529934646.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529934646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529934646 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1cncnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 25, 40, 44, 44, 35, 44, 44, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 25, 25, 40, 40, 44, 40, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 212 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529934646 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529934646 Building ZINC000529957469 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529957469 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/606 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529957469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529957469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529957469 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 35, 17, 17, 17, 35, 17, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 35, 35, 105, 17, 17, 17, 35, 35, 105, 17, 17] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 424 number of broken/clashed sets: 195 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/607 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/607' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529957469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529957469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529957469 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 39, 16, 16, 16, 35, 16, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 39, 39, 117, 16, 16, 16, 35, 35, 105, 16, 16] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 460 number of broken/clashed sets: 214 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529957469 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 Building ZINC000529957469 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529957469 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 606) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529957469.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529957469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529957469 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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: [6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 7, 17, 17, 17, 17, 35, 17, 17, 17, 35, 17, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 35, 35, 105, 17, 17, 17, 35, 35, 105, 17, 17] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 424 number of broken/clashed sets: 195 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 607) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529957469.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529957469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000529957469 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 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: [4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 5, 16, 16, 16, 16, 39, 16, 16, 16, 35, 16, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 39, 39, 117, 16, 16, 16, 35, 35, 105, 16, 16] 450 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 460 number of broken/clashed sets: 214 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529957469 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529957469 Building ZINC000529965231 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529965231 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/608 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/608' -> `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@](C)(CO)[C@](C)(CO)C1) `ZINC000529965231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529965231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529965231 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 44, 16, 16, 16, 39, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 44, 44, 132, 16, 16, 16, 39, 39, 117, 16, 16] 450 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 512 number of broken/clashed sets: 239 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/609 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/609' -> `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@](C)(CO)[C@](C)(CO)C1) `ZINC000529965231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529965231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529965231 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 8, 15, 15, 15, 15, 40, 15, 15, 15, 42, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 40, 40, 120, 15, 15, 15, 42, 42, 126, 15, 15] 450 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]) total number of confs: 517 number of broken/clashed sets: 237 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529965231 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 Building ZINC000529965231 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529965231 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 608) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529965231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529965231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529965231 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 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: [1, 1, 1, 1, 1, 1, 1, 4, 8, 16, 16, 16, 16, 44, 16, 16, 16, 39, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 44, 44, 132, 16, 16, 16, 39, 39, 117, 16, 16] 450 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 512 number of broken/clashed sets: 239 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 609) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)C1) `ZINC000529965231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529965231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000529965231 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@](C)(CO)[C@](C)(CO)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', 'O.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', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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, 7, 7, 7] 2 hydrogens need rotated 450 conformations in input total number of sets (complete confs): 450 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 4, 8, 15, 15, 15, 15, 40, 15, 15, 15, 42, 15, 2, 2, 2, 2, 2, 2, 2, 2, 2, 15, 15, 15, 15, 15, 40, 40, 120, 15, 15, 15, 42, 42, 126, 15, 15] 450 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]) total number of confs: 517 number of broken/clashed sets: 237 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529965231 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529965231 Building ZINC000529970257 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529970257 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/610 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000529970257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529970257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529970257 none CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 28, 13, 13, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 13, 13, 13, 13, 13, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/611 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/611' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000529970257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529970257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529970257 none CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 26, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529970257 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 Building ZINC000529970257 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529970257 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 610) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000529970257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529970257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529970257 none CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 28, 13, 13, 13, 13, 5, 13, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 13, 13, 13, 13, 13, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 99 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 611) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000529970257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529970257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000529970257 none CC(C)O[C@@]1(C)C[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 26, 13, 13, 13, 13, 4, 13, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 88 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529970257 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529970257 Building ZINC000529961245 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529961245 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/612 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CO)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO) `ZINC000529961245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529961245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529961245 none C[C@]1(CO)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 35, 18, 4, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 18, 18, 38, 18, 18, 18, 35, 35, 105, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 38, 38, 114] 450 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: 446 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/613 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/613' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(CO)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO) `ZINC000529961245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529961245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529961245 none C[C@]1(CO)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 42, 19, 4, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 19, 38, 19, 19, 19, 42, 42, 126, 19, 19, 3, 3, 1, 3, 3, 19, 19, 19, 19, 19, 38, 38, 114] 450 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 484 number of broken/clashed sets: 211 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529961245 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 Building ZINC000529961245 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000529961245 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 612) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@]1(CO)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO) `ZINC000529961245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000529961245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529961245 none C[C@]1(CO)CN(C(=O)[C@@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [18, 18, 18, 35, 18, 4, 1, 7, 1, 1, 1, 3, 3, 3, 3, 3, 18, 18, 18, 18, 38, 18, 18, 18, 35, 35, 105, 18, 18, 3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 38, 38, 114] 450 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: 446 number of broken/clashed sets: 197 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 613) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@]1(CO)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO) `ZINC000529961245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000529961245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000529961245 none C[C@]1(CO)CN(C(=O)[C@]([O-])([SiH3])c2ccccc2)C[C@@]1(C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 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, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [19, 19, 19, 42, 19, 4, 1, 7, 1, 1, 1, 3, 3, 1, 3, 3, 19, 19, 19, 19, 38, 19, 19, 19, 42, 42, 126, 19, 19, 3, 3, 1, 3, 3, 19, 19, 19, 19, 19, 38, 38, 114] 450 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 484 number of broken/clashed sets: 211 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000529961245 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000529961245 Building ZINC000121366830 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121366830 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/614 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1) `ZINC000121366830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121366830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121366830 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 3, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/615 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/615' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1) `ZINC000121366830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121366830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121366830 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 21, 21, 21, 21, 21, 7, 3, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121366830 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 Building ZINC000121366830 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121366830 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 614) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1) `ZINC000121366830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121366830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121366830 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 6, 21, 21, 21, 21, 21, 6, 3, 13, 13, 13, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 615) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1) `ZINC000121366830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121366830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121366830 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc3[nH]nnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 6, 8, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 21, 21, 21, 21, 21, 7, 3, 12, 12, 12, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121366830 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121366830 Building ZINC000752411777 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411777 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/616 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411777 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 36, 36, 11, 36, 4, 1, 4, 1, 1, 1, 2, 2, 2, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/617 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/617' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411777 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 12, 40, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 40, 40, 40, 40, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411777 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 Building ZINC000752411777 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411777 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 616) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/616: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411777.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411777 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 36, 36, 36, 11, 36, 4, 1, 4, 1, 1, 1, 2, 2, 2, 36, 36, 36, 36, 50, 50, 50, 36, 36, 36, 36, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 36, 36, 36, 36, 36] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 143 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 617) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/617: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411777.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411777 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 12, 40, 4, 1, 4, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 50, 50, 50, 40, 40, 40, 40, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411777 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411777 Building ZINC000752411779 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411779 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/618 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411779 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 9, 40, 4, 1, 4, 1, 1, 1, 2, 2, 2, 40, 40, 40, 40, 50, 50, 50, 40, 40, 40, 40, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/619 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/619' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411779 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 34, 34, 34, 9, 34, 3, 1, 3, 1, 1, 1, 2, 2, 2, 34, 34, 34, 34, 50, 50, 50, 34, 34, 34, 34, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411779 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 Building ZINC000752411779 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411779 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 618) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411779 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 50, 40, 40, 40, 9, 40, 4, 1, 4, 1, 1, 1, 2, 2, 2, 40, 40, 40, 40, 50, 50, 50, 40, 40, 40, 40, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 40, 40, 40, 40, 40] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 141 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 619) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411779 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 34, 34, 34, 9, 34, 3, 1, 3, 1, 1, 1, 2, 2, 2, 34, 34, 34, 34, 50, 50, 50, 34, 34, 34, 34, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 34, 34, 34, 34, 34] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 150 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411779 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411779 Building ZINC000752411781 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411781 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/620 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411781 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 39, 10, 34, 3, 1, 3, 1, 1, 1, 2, 2, 2, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/621 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/621' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411781 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 35, 35, 35, 7, 31, 3, 1, 3, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 35, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411781 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 Building ZINC000752411781 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411781 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 620) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411781 none CC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 39, 10, 34, 3, 1, 3, 1, 1, 1, 2, 2, 2, 39, 39, 39, 39, 50, 50, 50, 39, 39, 39, 39, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 39, 39, 39, 39, 39] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 621) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1) `ZINC000752411781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411781 none CC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 50, 35, 35, 35, 7, 31, 3, 1, 3, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 50, 50, 50, 35, 35, 35, 35, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 136 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411781 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411781 Building ZINC000752411782 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411782 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/622 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411782 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 50, 41, 41, 41, 10, 41, 4, 1, 4, 1, 1, 1, 2, 2, 2, 41, 41, 41, 41, 50, 50, 50, 41, 41, 41, 41, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/623 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/623' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411782 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 50, 41, 41, 41, 8, 41, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 50, 50, 50, 41, 41, 41, 41, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411782 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 Building ZINC000752411782 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000752411782 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 622) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/622: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000752411782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411782 none CC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 50, 41, 41, 41, 10, 41, 4, 1, 4, 1, 1, 1, 2, 2, 2, 41, 41, 41, 41, 50, 50, 50, 41, 41, 41, 41, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 139 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 623) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/623: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1) `ZINC000752411782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000752411782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000752411782 none CC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.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'] dock atom type numbers: [5, 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, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 50, 41, 41, 41, 8, 41, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 50, 50, 50, 41, 41, 41, 41, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42]) total number of confs: 130 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000752411782 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000752411782 Building ZINC000652919514 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652919514 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/624 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1) `ZINC000652919514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652919514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919514 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 22, 10, 20, 24, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 22, 22, 66, 20, 20, 24, 24, 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]) total number of confs: 283 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/625 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/625' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1) `ZINC000652919514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652919514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919514 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 9, 9, 18, 9, 19, 24, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 3, 18, 18, 54, 19, 19, 24, 24, 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]) total number of confs: 253 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652919514 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 Building ZINC000652919514 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652919514 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 624) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/624: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1) `ZINC000652919514.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652919514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919514 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 6, 16, 16, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 22, 10, 20, 24, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 6, 3, 22, 22, 66, 20, 20, 24, 24, 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]) total number of confs: 283 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 625) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1) `ZINC000652919514.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652919514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919514 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 9, 9, 18, 9, 19, 24, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 3, 18, 18, 54, 19, 19, 24, 24, 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]) total number of confs: 253 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652919514 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919514 Building ZINC000652919515 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652919515 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/626 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1) `ZINC000652919515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652919515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919515 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 9, 17, 21, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 17, 17, 51, 17, 17, 21, 21, 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]) total number of confs: 235 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/627 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1) `ZINC000652919515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652919515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919515 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 21, 10, 20, 23, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 21, 21, 63, 20, 20, 23, 23, 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]) total number of confs: 265 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652919515 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 Building ZINC000652919515 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652919515 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 626) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1) `ZINC000652919515.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652919515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919515 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 9, 9, 17, 9, 17, 21, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 17, 17, 51, 17, 17, 21, 21, 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]) total number of confs: 235 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 627) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1) `ZINC000652919515.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652919515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC000652919515 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 15, 6, 6, 1, 1, 1, 1, 3, 3, 3, 10, 10, 21, 10, 20, 23, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 3, 21, 21, 63, 20, 20, 23, 23, 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]) total number of confs: 265 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652919515 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652919515 Building ZINC000928892199 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892199 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/628 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892199 none C[C@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 12, 12, 12, 12, 12, 12, 12, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/629 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/629' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892199 none C[C@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 15, 15, 15, 15, 15, 15, 15, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892199 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 Building ZINC000928892199 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892199 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 628) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/628: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892199 none C[C@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 7, 12, 12, 12, 12, 12, 12, 12, 3, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 629) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892199 none C[C@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 8, 15, 15, 15, 15, 15, 15, 15, 4, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892199 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892199 Building ZINC000928892200 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892200 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/630 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892200 none C[C@@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 15, 15, 15, 15, 15, 15, 15, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/631 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/631' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892200 none C[C@@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 13, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 13, 13, 13, 13, 13, 13, 13, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892200 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 Building ZINC000928892200 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892200 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 630) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892200.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892200 none C[C@@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 6, 15, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 17, 17, 17, 9, 15, 15, 15, 15, 15, 15, 15, 4, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 631) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/631: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892200.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892200 none C[C@@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 13, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 7, 13, 13, 13, 13, 13, 13, 13, 3, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892200 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892200 Building ZINC000928892201 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892201 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/632 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892201 none C[C@@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 12, 12, 12, 12, 12, 12, 12, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/633 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/633' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892201 none C[C@@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 7, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 14, 14, 14, 14, 14, 14, 14, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892201 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 Building ZINC000928892201 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892201 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 632) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/632: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892201.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892201 none C[C@@H]1COC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 15, 15, 15, 8, 12, 12, 12, 12, 12, 12, 12, 3, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 633) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/633: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892201.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892201 none C[C@@H]1COC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 7, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 14, 14, 14, 14, 14, 14, 14, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892201 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892201 Building ZINC000928892202 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892202 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/634 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892202 none C[C@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 7, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 14, 14, 14, 14, 14, 14, 14, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/635 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/635' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892202 none C[C@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 12, 12, 12, 12, 12, 12, 12, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892202 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 Building ZINC000928892202 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000928892202 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 634) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/634: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000928892202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892202 none C[C@H]1COC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 7, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 16, 16, 16, 9, 14, 14, 14, 14, 14, 14, 14, 4, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 635) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/635: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000928892202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000928892202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000928892202 none C[C@H]1COC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 5, 12, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 14, 14, 14, 8, 12, 12, 12, 12, 12, 12, 12, 3, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000928892202 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000928892202 Building ZINC000530192428 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530192428 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/636 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530192428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192428 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 26, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 45, 45, 45, 45, 45, 26, 26, 9, 9, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/637 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/637' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530192428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192428 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 29, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 44, 44, 44, 44, 44, 29, 29, 11, 11, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530192428 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 Building ZINC000530192428 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530192428 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 636) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/636: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192428.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530192428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192428 none CCOC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 44, 26, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 45, 45, 45, 45, 45, 26, 26, 9, 9, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 126 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 637) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/637: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192428.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530192428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192428 none CCOC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 29, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 11, 11, 11, 44, 44, 44, 44, 44, 29, 29, 11, 11, 3, 3, 3, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 145 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530192428 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192428 Building ZINC000530192429 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530192429 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/638 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530192429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192429 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 27, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 44, 44, 44, 44, 44, 27, 27, 9, 9, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/639 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/639' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530192429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192429 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 39, 24, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 42, 42, 42, 42, 42, 24, 24, 7, 7, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530192429 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 Building ZINC000530192429 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530192429 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 638) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192429.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530192429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192429 none CCOC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 41, 27, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 3, 3, 3, 3, 3, 9, 9, 9, 44, 44, 44, 44, 44, 27, 27, 9, 9, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 136 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 639) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1) `ZINC000530192429.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530192429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000530192429 none CCOC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc[nH]2)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', '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, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 6, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 39, 24, 7, 7, 7, 7, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 7, 7, 7, 42, 42, 42, 42, 42, 24, 24, 7, 7, 4, 4, 4, 7, 7, 7, 7] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 127 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530192429 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530192429 Building ZINC000451053781 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000451053781 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/640 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000451053781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053781 none O=C(N1CCC[C@@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 17, 17, 17, 17, 17, 17, 38, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 38, 38, 46, 46, 138, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 327 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/641 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000451053781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053781 none O=C(N1CCC[C@@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 35, 43, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 129, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 313 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000451053781 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 Building ZINC000451053781 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000451053781 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 640) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCC[C@@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000451053781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053781 none O=C(N1CCC[C@@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 17, 17, 17, 17, 17, 17, 38, 46, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 38, 38, 46, 46, 138, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 327 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 641) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCC[C@@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000451053781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053781 none O=C(N1CCC[C@@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 35, 43, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 129, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 313 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000451053781 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053781 Building ZINC000451053782 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000451053782 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/642 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000451053782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053782 none O=C(N1CCC[C@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 35, 43, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 129, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 310 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/643 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/643' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000451053782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053782 none O=C(N1CCC[C@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 17, 17, 17, 17, 17, 17, 40, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 40, 40, 47, 47, 141, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 330 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000451053782 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 Building ZINC000451053782 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000451053782 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 642) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCC[C@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000451053782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053782 none O=C(N1CCC[C@H]1CCO)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 17, 17, 17, 17, 17, 17, 35, 43, 1, 1, 1, 4, 4, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 35, 35, 43, 43, 129, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 310 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 643) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCC[C@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000451053782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000451053782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000451053782 none O=C(N1CCC[C@H]1CCO)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 7, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 1, 10, 17, 17, 17, 17, 17, 17, 40, 47, 1, 1, 1, 3, 3, 1, 1, 3, 3, 17, 17, 17, 17, 17, 17, 40, 40, 47, 47, 141, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 330 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000451053782 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000451053782 Building ZINC000652921930 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652921930 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/644 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652921930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652921930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921930 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 37, 15, 32, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 35, 35, 35, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/645 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652921930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652921930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921930 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 19, 19, 39, 19, 34, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 117, 35, 35, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 402 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652921930 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 Building ZINC000652921930 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652921930 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 644) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652921930.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652921930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921930 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 37, 15, 32, 38, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 37, 37, 111, 35, 35, 35, 38] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 375 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 645) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF) `ZINC000652921930.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652921930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921930 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 19, 19, 39, 19, 34, 42, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 39, 39, 117, 35, 35, 42, 42] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 402 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652921930 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921930 Building ZINC000652921931 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652921931 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/646 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652921931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652921931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921931 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 20, 20, 38, 20, 35, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 396 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/647 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/647' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652921931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652921931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921931 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 36, 14, 32, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 36, 36, 108, 34, 34, 37, 35] 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]) total number of confs: 356 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652921931 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 Building ZINC000652921931 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652921931 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 646) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652921931.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652921931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921931 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 20, 20, 38, 20, 35, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 38, 38, 114, 36, 36, 43, 43] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 396 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 647) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF) `ZINC000652921931.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652921931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000652921931 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](CO)CCF NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 5, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 5, 14, 14, 36, 14, 32, 37, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 36, 36, 108, 34, 34, 37, 35] 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]) total number of confs: 356 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652921931 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652921931 Building ZINC000530302234 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530302234 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/648 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1) `ZINC000530302234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530302234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000530302234 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 2, 8, 8, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/649 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/649' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1) `ZINC000530302234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530302234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000530302234 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 2, 8, 8, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530302234 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 Building ZINC000530302234 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000530302234 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 648) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/648: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1) `ZINC000530302234.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000530302234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000530302234 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 2, 8, 8, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 649) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/649: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1) `ZINC000530302234.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000530302234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000530302234 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ncccc2F)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 8, 1, 1, 1, 1, 15, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 2, 8, 8, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000530302234 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000530302234 Building ZINC000121718383 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121718383 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/650 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1) `ZINC000121718383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121718383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121718383 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 14, 14, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/651 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/651' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1) `ZINC000121718383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121718383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121718383 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 20, 20, 20, 20, 20, 5, 5, 15, 15, 15, 15, 15, 5, 2, 14, 14, 20, 20, 20, 20, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121718383 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 Building ZINC000121718383 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121718383 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 650) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1) `ZINC000121718383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121718383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121718383 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 19, 19, 19, 19, 19, 5, 5, 15, 15, 15, 15, 15, 5, 2, 14, 14, 19, 19, 19, 19, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 651) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1) `ZINC000121718383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121718383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121718383 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccccn2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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: [15, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 14, 20, 20, 20, 20, 20, 5, 5, 15, 15, 15, 15, 15, 5, 2, 14, 14, 20, 20, 20, 20, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121718383 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121718383 Building ZINC000121725609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121725609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/652 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1) `ZINC000121725609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121725609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121725609 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 16, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/653 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/653' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1) `ZINC000121725609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121725609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121725609 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121725609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 Building ZINC000121725609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121725609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 652) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1) `ZINC000121725609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121725609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121725609 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 16, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 653) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1) `ZINC000121725609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121725609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121725609 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccncc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 18, 18, 18, 5, 5, 13, 13, 13, 13, 13, 5, 2, 12, 12, 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]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121725609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121725609 Building ZINC000121733044 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121733044 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/654 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1) `ZINC000121733044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121733044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121733044 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/655 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/655' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1) `ZINC000121733044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121733044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121733044 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121733044 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 Building ZINC000121733044 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121733044 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 654) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1) `ZINC000121733044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121733044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121733044 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 655) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1) `ZINC000121733044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121733044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000121733044 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2cccnc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 22, 22, 22, 5, 5, 11, 11, 11, 11, 11, 5, 2, 12, 12, 22, 22, 22, 22, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121733044 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121733044 Building ZINC000121794820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121794820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/656 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000121794820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121794820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000121794820 none COc1cccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 27, 27, 27, 27, 7, 4, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 27, 27, 27, 7, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/657 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/657' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000121794820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121794820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000121794820 none COc1cccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 27, 27, 27, 27, 27, 7, 4, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 27, 27, 27, 7, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121794820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 Building ZINC000121794820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121794820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 656) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1cccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000121794820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121794820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000121794820 none COc1cccnc1N(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens 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, 27, 27, 27, 27, 7, 4, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 27, 27, 27, 7, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 657) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1cccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000121794820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121794820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000121794820 none COc1cccnc1N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 27, 27, 27, 27, 27, 27, 7, 4, 7, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 27, 27, 27, 7, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121794820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121794820 Building ZINC000121795888 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121795888 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/658 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2)cn1) `ZINC000121795888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121795888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000121795888 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 6, 8, 14, 14, 8, 8, 7, 7, 23, 23, 23, 23, 23, 7, 3, 8, 8, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/659 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2)cn1) `ZINC000121795888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121795888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000121795888 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 13, 14, 8, 8, 7, 7, 25, 25, 25, 25, 25, 7, 3, 8, 8, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121795888 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 Building ZINC000121795888 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121795888 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 658) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2)cn1) `ZINC000121795888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121795888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000121795888 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 6, 8, 14, 14, 8, 8, 7, 7, 23, 23, 23, 23, 23, 7, 3, 8, 8, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 659) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=O)cc2)cn1) `ZINC000121795888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121795888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000121795888 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(C(N)=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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 11, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 8, 8, 3, 6, 13, 14, 8, 8, 7, 7, 25, 25, 25, 25, 25, 7, 3, 8, 8, 14, 14, 8, 8, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121795888 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121795888 Building ZINC000152342292 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152342292 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/660 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000152342292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152342292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000152342292 none COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 17, 29, 17, 17, 17, 17, 17, 8, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 29, 17, 17, 17, 17, 17, 17, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/661 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/661' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000152342292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152342292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000152342292 none COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 17, 26, 17, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 17, 17, 17, 17, 17, 17, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000152342292 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 Building ZINC000152342292 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000152342292 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 660) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000152342292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000152342292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000152342292 none COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 17, 29, 17, 17, 17, 17, 17, 8, 17, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 29, 29, 29, 17, 17, 17, 17, 17, 17, 4, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 661) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000152342292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000152342292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000152342292 none COC(=O)[C@@H]1CCC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 17, 26, 17, 17, 17, 17, 17, 6, 17, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 17, 17, 17, 17, 17, 17, 4, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000152342292 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000152342292 Building ZINC000121809956 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121809956 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/662 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121809956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121809956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121809956 none CCOC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 17, 9, 17, 7, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 13, 3, 31, 31, 31, 31, 31, 9, 9, 9, 7, 7, 4, 3, 13, 13, 13, 13, 13, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/663 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/663' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121809956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121809956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121809956 none CCOC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 6, 15, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 26, 26, 26, 26, 26, 6, 6, 6, 5, 5, 3, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121809956 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 Building ZINC000121809956 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121809956 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 662) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121809956.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121809956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121809956 none CCOC(=O)[C@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 17, 9, 17, 7, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 13, 3, 31, 31, 31, 31, 31, 9, 9, 9, 7, 7, 4, 3, 13, 13, 13, 13, 13, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 663) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121809956.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121809956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121809956 none CCOC(=O)[C@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 15, 6, 15, 5, 6, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 10, 4, 26, 26, 26, 26, 26, 6, 6, 6, 5, 5, 3, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121809956 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121809956 Building ZINC000121810114 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121810114 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/664 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121810114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121810114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121810114 none CCOC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 16, 8, 16, 6, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 10, 4, 28, 28, 28, 28, 28, 8, 8, 8, 6, 6, 4, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/665 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/665' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121810114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121810114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121810114 none CCOC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 17, 9, 17, 7, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 13, 3, 31, 31, 31, 31, 31, 9, 9, 9, 7, 7, 4, 3, 13, 13, 13, 13, 13, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121810114 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 Building ZINC000121810114 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000121810114 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 664) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121810114.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000121810114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121810114 none CCOC(=O)[C@@H](C)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 16, 8, 16, 6, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 10, 4, 28, 28, 28, 28, 28, 8, 8, 8, 6, 6, 4, 4, 10, 10, 10, 10, 10, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 665) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000121810114.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000121810114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000121810114 none CCOC(=O)[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 20, 17, 9, 17, 7, 9, 9, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 13, 3, 31, 31, 31, 31, 31, 9, 9, 9, 7, 7, 4, 3, 13, 13, 13, 13, 13, 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]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000121810114 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000121810114 Building ZINC000652954014 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652954014 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/666 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)CCCOC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652954014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652954014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000652954014 none O=C(NCC[C@@]1(O)CCCOC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 24, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 24, 24, 26, 26, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 326 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/667 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/667' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)CCCOC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652954014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652954014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000652954014 none O=C(NCC[C@@]1(O)CCCOC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 21, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 4, 4, 4, 5, 21, 21, 24, 24, 150, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 332 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652954014 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 Building ZINC000652954014 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652954014 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 666) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/666: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)CCCOC1)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652954014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652954014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000652954014 none O=C(NCC[C@@]1(O)CCCOC1)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 24, 34, 50, 50, 50, 50, 50, 50, 1, 1, 1, 3, 3, 1, 1, 3, 3, 5, 24, 24, 26, 26, 150, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 6, 3, 3] 300 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 326 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 667) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC[C@@]1(O)CCCOC1)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652954014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652954014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC000652954014 none O=C(NCC[C@@]1(O)CCCOC1)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 1, 5, 5, 21, 31, 50, 50, 50, 50, 50, 50, 1, 1, 1, 4, 4, 1, 4, 4, 4, 5, 21, 21, 24, 24, 150, 50, 50, 50, 50, 50, 50, 50, 50, 4, 4, 8, 4, 4] 300 rigid atoms, others: [1, 12, 13, 14] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 332 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652954014 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652954014 Building ZINC000304235277 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304235277 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/668 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000304235277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304235277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000304235277 none C[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [30, 19, 30, 30, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 90, 22, 22, 15, 15, 2, 6, 7, 7, 6, 7, 7, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/669 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/669' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000304235277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304235277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000304235277 none C[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [33, 20, 33, 33, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 99, 22, 22, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304235277 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 Building ZINC000304235277 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304235277 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 668) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000304235277.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304235277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000304235277 none C[C@H](O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [30, 19, 30, 30, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 6, 7, 7, 6, 30, 30, 30, 90, 22, 22, 15, 15, 2, 6, 7, 7, 6, 7, 7, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 669) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/669: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000304235277.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304235277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000304235277 none C[C@H](O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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: [33, 20, 33, 33, 15, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 33, 33, 33, 99, 22, 22, 15, 15, 3, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304235277 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304235277 Building ZINC000374625089 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000374625089 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/670 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000374625089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000374625089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000374625089 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/671 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/671' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000374625089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000374625089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000374625089 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000374625089 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 Building ZINC000374625089 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000374625089 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 670) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000374625089.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000374625089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000374625089 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 6, 10, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 11] 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: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 671) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1) `ZINC000374625089.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000374625089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000374625089 none Cn1cc([C@]([O-])([SiH3])C(=O)N2C[C@@H]3CCC[C@H](N)[C@H]3C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 10, 5, 7, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 6, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000374625089 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000374625089 Building ZINC000986067796 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000986067796 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/672 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000986067796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000986067796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067796 none C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 14, 28, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 28, 28, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/673 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/673' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000986067796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000986067796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067796 none C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 17, 29, 50, 50, 50, 50, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000986067796 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 Building ZINC000986067796 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000986067796 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 672) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000986067796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000986067796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067796 none C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 14, 28, 50, 50, 50, 50, 5, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 28, 28, 50, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 130 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 673) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000986067796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000986067796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067796 none C[C@H]1[C@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 17, 29, 50, 50, 50, 50, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 29, 29, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000986067796 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067796 Building ZINC000986067798 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000986067798 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/674 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000986067798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000986067798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067798 none C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 22, 36, 50, 50, 50, 50, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 36, 36, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/675 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000986067798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000986067798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067798 none C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 30, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 30, 30, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000986067798 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 Building ZINC000986067798 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000986067798 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 674) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC000986067798.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000986067798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067798 none C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 22, 36, 50, 50, 50, 50, 7, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 22, 36, 36, 50, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 157 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 675) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC000986067798.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000986067798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000986067798 none C[C@@H]1[C@@H](NCc2cnon2)CCN1C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', 'N.3', 'C.3', 'C.2', 'C.2', 'N.2', 'O.3', 'N.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'] dock atom type numbers: [5, 5, 7, 5, 7, 10, 5, 1, 1, 8, 12, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 18, 30, 50, 50, 50, 50, 6, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 30, 30, 50, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 133 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000986067798 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000986067798 Building ZINC000304934579 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304934579 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/676 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O) `ZINC000304934579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304934579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934579 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 31, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 31, 31, 43, 43, 43, 129] 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]) total number of confs: 311 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/677 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/677' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O) `ZINC000304934579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304934579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934579 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 31, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 31, 31, 41, 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]) total number of confs: 294 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304934579 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 Building ZINC000304934579 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000304934579 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 676) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O) `ZINC000304934579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000304934579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934579 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 11, 11, 31, 43, 43, 43, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 31, 31, 43, 43, 43, 129] 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]) total number of confs: 311 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 677) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O) `ZINC000304934579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000304934579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000304934579 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)C[C@H](C)O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 10, 10, 31, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 10, 31, 31, 41, 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]) total number of confs: 294 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000304934579 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000304934579 Building ZINC000305113669 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305113669 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/678 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305113669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000305113669 none O=C(NCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 24, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 18, 18, 24, 24, 72, 10, 15, 15, 10, 15, 15, 10] 150 rigid atoms, others: [8, 1, 6, 7] set([0, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/679 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305113669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000305113669 none O=C(NCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 24, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 18, 18, 24, 24, 72, 10, 15, 15, 15, 15, 15, 10] 150 rigid atoms, others: [8, 1, 6, 7] set([0, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305113669 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 Building ZINC000305113669 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305113669 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 678) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305113669.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000305113669 none O=C(NCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 24, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 18, 18, 24, 24, 72, 10, 15, 15, 10, 15, 15, 10] 150 rigid atoms, others: [8, 1, 6, 7] set([0, 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]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 679) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305113669.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305113669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000305113669 none O=C(NCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 18, 24, 1, 1, 1, 10, 10, 10, 10, 15, 15, 10, 15, 15, 10, 4, 18, 18, 24, 24, 72, 10, 15, 15, 15, 15, 15, 10] 150 rigid atoms, others: [8, 1, 6, 7] set([0, 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]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305113669 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305113669 Building ZINC000305118124 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305118124 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/680 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305118124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305118124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000305118124 none O=C(N1CC(O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 14, 14, 14, 14, 1, 1, 1, 12, 12, 12, 12, 28, 28, 12, 28, 28, 12, 14, 14, 14, 42, 14, 14, 12, 28, 28, 12, 28, 28, 12] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/681 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/681' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC(O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305118124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305118124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000305118124 none O=C(N1CC(O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 14, 14, 14, 14, 1, 1, 1, 12, 12, 12, 12, 31, 31, 12, 31, 31, 12, 14, 14, 14, 42, 14, 14, 12, 31, 31, 12, 31, 31, 12] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305118124 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 Building ZINC000305118124 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305118124 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 680) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC(O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305118124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305118124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000305118124 none O=C(N1CC(O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 14, 14, 14, 14, 1, 1, 1, 12, 12, 12, 12, 28, 28, 12, 28, 28, 12, 14, 14, 14, 42, 14, 14, 12, 28, 28, 12, 28, 28, 12] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 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]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 681) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC(O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305118124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305118124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000305118124 none O=C(N1CC(O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 14, 14, 14, 14, 1, 1, 1, 12, 12, 12, 12, 31, 31, 12, 31, 31, 12, 14, 14, 14, 42, 14, 14, 12, 31, 31, 12, 31, 31, 12] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305118124 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305118124 Building ZINC000305148610 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305148610 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/682 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305148610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305148610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000305148610 none O=C(NCCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 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, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 21, 28, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 4, 16, 16, 25, 25, 26, 26, 84, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/683 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/683' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305148610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305148610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000305148610 none O=C(NCCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 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, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 21, 28, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 4, 16, 16, 25, 25, 26, 26, 84, 6, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305148610 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 Building ZINC000305148610 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305148610 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 682) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/682: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305148610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305148610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000305148610 none O=C(NCCCO)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 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, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 21, 28, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 4, 16, 16, 25, 25, 26, 26, 84, 6, 8, 8, 6, 8, 8, 6] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 683) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/683: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305148610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305148610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000305148610 none O=C(NCCCO)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 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, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 16, 21, 28, 1, 1, 1, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 4, 16, 16, 25, 25, 26, 26, 84, 6, 8, 8, 8, 8, 8, 6] 150 rigid atoms, others: [8, 1, 9, 7] set([0, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 234 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305148610 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305148610 Building ZINC000305156151 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305156151 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/684 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305156151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156151 none C[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 25, 29, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 29, 29, 87, 5, 9, 15, 15, 9, 15, 15, 9] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/685 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/685' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305156151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156151 none C[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 23, 27, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 12, 12, 12, 25, 25, 27, 27, 81, 4, 10, 14, 14, 14, 14, 14, 10] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305156151 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 Building ZINC000305156151 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305156151 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 684) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305156151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156151 none C[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 25, 29, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 29, 29, 87, 5, 9, 15, 15, 9, 15, 15, 9] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 685) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305156151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156151 none C[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 23, 27, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 12, 12, 12, 25, 25, 27, 27, 81, 4, 10, 14, 14, 14, 14, 14, 10] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 242 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305156151 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156151 Building ZINC000305156155 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305156155 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/686 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305156155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156155 none C[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 23, 27, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 12, 12, 12, 25, 25, 27, 27, 81, 4, 10, 14, 14, 10, 14, 14, 10] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/687 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/687' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305156155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156155 none C[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 25, 29, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 29, 29, 87, 5, 9, 15, 15, 9, 15, 15, 9] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305156155 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 Building ZINC000305156155 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305156155 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 686) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/686: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305156155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156155 none C[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 12, 12, 23, 27, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 14, 14, 10, 14, 14, 10, 12, 12, 12, 25, 25, 27, 27, 81, 4, 10, 14, 14, 10, 14, 14, 10] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 687) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/687: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305156155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305156155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305156155 none C[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 13, 13, 25, 29, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 15, 15, 9, 15, 15, 9, 13, 13, 13, 25, 25, 29, 29, 87, 5, 9, 15, 15, 9, 15, 15, 9] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305156155 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305156155 Building ZINC000452262496 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452262496 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/688 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452262496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452262496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262496 none C[C@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 40, 40, 46, 47, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 47, 47, 141, 30, 30, 17, 17, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/689 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/689' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452262496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452262496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262496 none C[C@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 43, 43, 48, 48, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 43, 48, 48, 48, 48, 144, 29, 29, 18, 18, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 397 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452262496 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 Building ZINC000452262496 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452262496 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 688) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/688: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452262496.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452262496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262496 none C[C@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 40, 40, 46, 47, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 47, 47, 141, 30, 30, 17, 17, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 689) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/689: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452262496.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452262496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262496 none C[C@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 43, 43, 48, 48, 18, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 43, 43, 43, 48, 48, 48, 48, 144, 29, 29, 18, 18, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 397 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452262496 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262496 Building ZINC000452262497 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452262497 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/690 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452262497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452262497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262497 none C[C@@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 48, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 48, 48, 144, 26, 26, 16, 16, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 407 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/691 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/691' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452262497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452262497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262497 none C[C@@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 40, 40, 46, 47, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 47, 47, 141, 30, 30, 17, 17, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452262497 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 Building ZINC000452262497 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452262497 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 690) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452262497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452262497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262497 none C[C@@H](CCO)CCNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 48, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 48, 48, 144, 26, 26, 16, 16, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 407 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 691) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452262497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452262497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452262497 none C[C@@H](CCO)CCNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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, 5, 7, 5, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 1 hydrogens 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, 25, 40, 40, 46, 47, 17, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 40, 40, 40, 46, 46, 47, 47, 141, 30, 30, 17, 17, 3, 4, 4, 4, 4, 4, 4] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 395 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452262497 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452262497 Building ZINC000305227163 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305227163 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/692 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305227163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227163 none C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 25, 33, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 33, 33, 99, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/693 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/693' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305227163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227163 none C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 26, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 30, 30, 90, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305227163 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 Building ZINC000305227163 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305227163 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 692) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227163.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305227163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227163 none C[C@@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 25, 33, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 33, 33, 99, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 693) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227163.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305227163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227163 none C[C@@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 26, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 30, 30, 90, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305227163 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227163 Building ZINC000305227164 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305227164 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/694 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305227164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227164 none C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 26, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 30, 30, 90, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/695 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/695' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305227164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227164 none C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 25, 33, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 33, 33, 99, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305227164 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 Building ZINC000305227164 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305227164 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 694) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305227164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227164 none C[C@H](CO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 26, 30, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 30, 30, 90, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 229 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 695) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305227164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305227164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305227164 none C[C@H](CO)CNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 13, 27, 25, 33, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 33, 33, 99, 13, 13, 2, 6, 6, 6, 6, 6, 6, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305227164 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305227164 Building ZINC000452385691 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385691 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/696 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/697 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/697' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/698 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/698' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/699 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/699' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385691 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 Building ZINC000452385691 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385691 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 696) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 697) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 698) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 699) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385691 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 Building ZINC000452385691 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385691 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 696) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 697) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 698) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 699) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385691 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 Building ZINC000452385691 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385691 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 696) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 697) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 698) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/698: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 19, 19, 19, 19, 19, 19, 30, 47, 48, 19, 3, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 30, 30, 47, 47, 48, 48, 144, 19, 19] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 699) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/699: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385691.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385691 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 27, 48, 48, 18, 4, 4, 4, 4, 4, 4, 3, 18, 18, 18, 18, 18, 18, 27, 27, 48, 48, 48, 48, 144, 18, 18] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385691 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385691 Building ZINC000452385694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/700 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/701 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/701' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/702 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/702' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/703 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/703' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 Building ZINC000452385694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 700) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 701) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 702) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 703) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 Building ZINC000452385694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 700) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 701) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 702) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 703) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 Building ZINC000452385694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452385694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 700) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 701) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 702) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/702: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 16, 16, 16, 16, 16, 16, 26, 45, 47, 16, 4, 4, 4, 4, 4, 4, 3, 16, 16, 16, 16, 16, 16, 26, 26, 45, 45, 47, 47, 141, 16, 16] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 703) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/703: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]1CCCN(CCCO)C1) `ZINC000452385694.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452385694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452385694 none Cn1cccc1[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(CCCO)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', 'C.3', 'N.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, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 6, 17, 17, 17, 17, 17, 17, 28, 45, 48, 17, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 48, 48, 144, 17, 17] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452385694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452385694 Building ZINC000452362225 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362225 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/704 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/705 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/705' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/706 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/706' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/707 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/707' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362225 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 Building ZINC000452362225 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362225 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 704) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 705) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 706) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 707) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362225 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 Building ZINC000452362225 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362225 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 704) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 705) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 706) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 707) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362225 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 Building ZINC000452362225 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362225 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 704) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 705) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 706) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/706: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 35, 35, 35, 35, 35, 35, 42, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 352 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 707) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/707: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362225.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362225 none O=C(NC[C@@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 34, 34, 34, 34, 34, 34, 42, 49, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 14, 14, 34, 34, 34, 34, 34, 34, 42, 42, 49, 49, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 350 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362225 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362225 Building ZINC000452362227 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362227 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/708 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/709 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/709' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/710 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/710' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/711 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/711' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362227 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 Building ZINC000452362227 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362227 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 708) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 709) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 710) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 711) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362227 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 Building ZINC000452362227 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362227 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 708) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 709) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 710) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 711) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362227 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 Building ZINC000452362227 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452362227 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 708) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 709) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 710) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 19, 35, 35, 35, 35, 35, 35, 42, 48, 49, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 35, 35, 35, 35, 35, 35, 42, 42, 48, 48, 49, 49, 147, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 711) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/711: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1) `ZINC000452362227.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452362227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC000452362227 none O=C(NC[C@H]1CCCN1CCCO)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 22, 36, 36, 36, 36, 36, 36, 43, 50, 50, 1, 1, 1, 3, 3, 1, 3, 3, 3, 15, 15, 36, 36, 36, 36, 36, 36, 43, 43, 50, 50, 50, 50, 150, 3, 3, 1, 3, 3] 150 rigid atoms, others: [1, 14, 15, 16] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452362227 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452362227 Building ZINC000652957830 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652957830 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/712 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652957830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957830 none C[C@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 23, 23, 44, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 44, 44, 50, 50, 150, 10, 10, 10, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 382 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/713 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/713' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652957830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957830 none C[C@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 8, 25, 25, 44, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 44, 44, 49, 49, 147, 8, 8, 8, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 381 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652957830 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 Building ZINC000652957830 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652957830 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 712) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652957830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957830 none C[C@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 23, 23, 44, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 44, 44, 50, 50, 150, 10, 10, 10, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 382 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 713) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652957830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957830 none C[C@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 8, 25, 25, 44, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 44, 44, 49, 49, 147, 8, 8, 8, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 381 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652957830 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957830 Building ZINC000652957831 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652957831 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/714 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652957831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957831 none C[C@@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 8, 25, 25, 44, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 44, 44, 49, 49, 147, 8, 8, 8, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 381 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/715 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/715' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652957831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957831 none C[C@@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 23, 23, 44, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 44, 44, 50, 50, 150, 10, 10, 10, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 382 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652957831 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 Building ZINC000652957831 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000652957831 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 714) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000652957831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957831 none C[C@@H](CCO)N(C)C(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [25, 8, 25, 25, 44, 49, 4, 8, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 25, 25, 25, 44, 44, 49, 49, 147, 8, 8, 8, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 381 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 715) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000652957831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000652957831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000652957831 none C[C@@H](CCO)N(C)C(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [23, 10, 23, 23, 44, 50, 5, 10, 1, 5, 1, 1, 1, 3, 3, 1, 1, 3, 3, 23, 23, 23, 44, 44, 50, 50, 150, 10, 10, 10, 3, 3, 6, 3, 3] 300 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 382 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000652957831 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000652957831 Building ZINC000452376813 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376813 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/716 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/717 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/717' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/718 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/718' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/719 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/719' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376813 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 Building ZINC000452376813 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376813 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 716) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 717) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 718) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 719) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376813 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 Building ZINC000452376813 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376813 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 716) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 717) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 718) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 719) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376813 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 Building ZINC000452376813 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376813 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 716) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 717) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 718) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/718: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 22, 35, 35, 35, 35, 35, 35, 42, 49, 50, 3, 3, 3, 3, 3, 3, 3, 14, 14, 35, 35, 35, 35, 35, 35, 42, 42, 49, 49, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 719) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/719: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@H]1CCCN1CCCO) `ZINC000452376813.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376813 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 34, 34, 34, 34, 34, 34, 42, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 345 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376813 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376813 Building ZINC000452376814 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376814 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/720 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/721 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/721' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/722 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/722' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/723 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/723' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376814 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 Building ZINC000452376814 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376814 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 720) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 721) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 722) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 723) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376814 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 Building ZINC000452376814 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376814 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 720) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 721) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 722) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 723) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376814 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 Building ZINC000452376814 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000452376814 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 720) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 721) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 722) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/722: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 43, 50, 50, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 35, 35, 35, 35, 35, 43, 43, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 723) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/723: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)NC[C@@H]1CCCN1CCCO) `ZINC000452376814.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000452376814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452376814 none Cn1cccc1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN1CCCO NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 10, 5, 5, 5, 12, 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, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 3, 3, 3, 23, 35, 35, 35, 35, 35, 35, 41, 50, 50, 3, 3, 3, 3, 3, 3, 3, 16, 16, 35, 35, 35, 35, 35, 35, 41, 41, 50, 50, 50, 50, 150] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 349 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452376814 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452376814 Building ZINC000305301416 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305301416 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/724 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305301416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305301416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305301416 none CCN(CCO)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 5, 8, 14, 19, 1, 5, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 10, 10, 10, 10, 10, 14, 14, 19, 19, 57, 6, 14, 14, 6, 14, 14, 6] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/725 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCO)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305301416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305301416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305301416 none CCN(CCO)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 4, 7, 14, 20, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 10, 10, 10, 10, 10, 14, 14, 20, 20, 60, 6, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 203 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305301416 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 Building ZINC000305301416 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305301416 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 724) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CCO)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305301416.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305301416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305301416 none CCN(CCO)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 5, 8, 14, 19, 1, 5, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 10, 10, 10, 10, 10, 14, 14, 19, 19, 57, 6, 14, 14, 6, 14, 14, 6] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 184 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 725) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(CCO)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305301416.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305301416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305301416 none CCN(CCO)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 12, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 4, 7, 14, 20, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 10, 10, 10, 10, 10, 14, 14, 20, 20, 60, 6, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 203 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305301416 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305301416 Building ZINC000452433587 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452433587 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/726 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452433587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452433587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433587 none C[C@@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 15, 38, 35, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 49, 49, 50, 50, 50, 50, 150, 15, 15, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 399 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/727 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452433587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452433587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433587 none C[C@@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452433587 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 Building ZINC000452433587 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452433587 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 726) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452433587.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452433587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433587 none C[C@@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 15, 38, 35, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 49, 49, 50, 50, 50, 50, 150, 15, 15, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 399 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 727) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452433587.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452433587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433587 none C[C@@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452433587 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433587 Building ZINC000452433588 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452433588 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/728 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452433588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452433588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433588 none C[C@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/729 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/729' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452433588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452433588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433588 none C[C@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 38, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 400 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452433588 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 Building ZINC000452433588 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452433588 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 728) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/728: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452433588.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452433588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433588 none C[C@H](CCCO)CNC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [37, 17, 37, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 729) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/729: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452433588.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452433588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452433588 none C[C@H](CCCO)CNC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 38, 36, 49, 50, 50, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 49, 49, 50, 50, 50, 50, 150, 17, 17, 3, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 400 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452433588 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452433588 Building ZINC000452565290 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452565290 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/730 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000452565290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452565290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452565290 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 22, 22, 22, 22, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 22, 46, 46, 46, 45, 45, 66, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 221 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/731 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/731' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000452565290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452565290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452565290 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 44, 44, 44, 44, 44, 66, 22, 22, 3, 3, 3, 3, 3, 3, 22, 22] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 215 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452565290 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 Building ZINC000452565290 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452565290 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 730) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000452565290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452565290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452565290 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [46, 45, 22, 22, 22, 22, 7, 1, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 22, 46, 46, 46, 45, 45, 66, 22, 22, 4, 4, 4, 4, 4, 4, 22, 22] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 221 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 731) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1) `ZINC000452565290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452565290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452565290 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2cc(F)ccc2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 15, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 22, 22, 22, 22, 6, 1, 6, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 22, 44, 44, 44, 44, 44, 66, 22, 22, 3, 3, 3, 3, 3, 3, 22, 22] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 215 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452565290 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452565290 Building ZINC000452566167 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452566167 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/732 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000452566167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452566167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452566167 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 27, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 37, 37, 37, 27, 27, 36, 12, 12, 6, 6, 12, 12] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/733 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/733' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000452566167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452566167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452566167 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 33, 33, 33, 28, 28, 42, 14, 14, 9, 9, 14, 14] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452566167 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 Building ZINC000452566167 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452566167 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 732) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000452566167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452566167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452566167 none COCC1(O)CN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 27, 12, 12, 12, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 12, 37, 37, 37, 27, 27, 36, 12, 12, 6, 6, 12, 12] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 154 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 733) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1) `ZINC000452566167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452566167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452566167 none COCC1(O)CN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)s2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 28, 14, 14, 14, 14, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 14, 33, 33, 33, 28, 28, 42, 14, 14, 9, 9, 14, 14] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 151 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452566167 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452566167 Building ZINC000452545409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452545409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/734 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(C)C) `ZINC000452545409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452545409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452545409 none CCN(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 18, 26, 6, 18, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 16, 16, 34, 34, 34, 34, 34, 26, 26, 26, 3, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/735 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/735' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(C)C) `ZINC000452545409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452545409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452545409 none CCN(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 30, 17, 30, 8, 17, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 16, 15, 40, 40, 40, 40, 40, 30, 30, 30, 4, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452545409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 Building ZINC000452545409 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452545409 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 734) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(C)C) `ZINC000452545409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452545409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452545409 none CCN(C)C(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cccn1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 18, 26, 6, 18, 3, 6, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 6, 16, 16, 34, 34, 34, 34, 34, 26, 26, 26, 3, 4, 4, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 735) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(C)C) `ZINC000452545409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452545409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000452545409 none CCN(C)C(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cccn1C)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 30, 17, 30, 8, 17, 4, 8, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 8, 16, 15, 40, 40, 40, 40, 40, 30, 30, 30, 4, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452545409 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452545409 Building ZINC000305635206 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635206 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/736 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635206 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 17, 18, 18, 10, 16, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 5, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 17, 51, 10, 10, 2, 5, 13, 13, 13, 13, 13, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/737 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/737' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635206 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635206 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 Building ZINC000305635206 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635206 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 736) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/736: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635206 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 17, 18, 18, 10, 16, 17, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 13, 5, 18, 18, 18, 18, 18, 18, 18, 18, 17, 17, 17, 51, 10, 10, 2, 5, 13, 13, 13, 13, 13, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 737) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/737: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635206 none CC[C@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 15, 15, 15, 15, 15, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635206 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635206 Building ZINC000305635207 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635207 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/738 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635207 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/739 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/739' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635207 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 13, 18, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 57, 13, 13, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635207 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 Building ZINC000305635207 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635207 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 738) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/738: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635207.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635207 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 739) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/739: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635207.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635207 none CC[C@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 13, 18, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 57, 13, 13, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635207 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635207 Building ZINC000305635209 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635209 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/740 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635209 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 15, 17, 17, 11, 15, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 45, 11, 11, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/741 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/741' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635209 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 16, 18, 18, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 20, 6, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 16, 48, 11, 11, 2, 6, 20, 20, 20, 20, 20, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635209 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 Building ZINC000305635209 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635209 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 740) grep: /scratch/xiaobo/365617/xds-8058088.97/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](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635209.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635209 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 15, 17, 17, 11, 15, 15, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 45, 11, 11, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 741) grep: /scratch/xiaobo/365617/xds-8058088.97/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](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635209.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635209 none CC[C@@H](C)[C@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 16, 18, 18, 11, 16, 16, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 20, 6, 18, 18, 18, 18, 18, 18, 18, 18, 16, 16, 16, 48, 11, 11, 2, 6, 20, 20, 20, 20, 20, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635209 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635209 Building ZINC000305635211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/742 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635211 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 13, 18, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 57, 13, 13, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/743 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/743' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635211 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 Building ZINC000305635211 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305635211 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 742) grep: /scratch/xiaobo/365617/xds-8058088.97/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](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305635211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635211 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 19, 19, 19, 13, 18, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 57, 13, 13, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 743) grep: /scratch/xiaobo/365617/xds-8058088.97/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](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305635211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305635211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000305635211 none CC[C@@H](C)[C@@](C)(O)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 13, 18, 18, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 16, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54, 13, 13, 2, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305635211 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305635211 Building ZINC000452622550 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622550 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/744 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622550 none CO[C@@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 44, 44, 44, 44, 44, 44, 44, 34, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 44, 44, 44, 44, 44, 44, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/745 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/745' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622550 none CO[C@@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 44, 44, 44, 44, 44, 44, 30, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 44, 44, 44, 44, 44, 44, 18, 18, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622550 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 Building ZINC000452622550 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622550 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 744) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622550 none CO[C@@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 44, 44, 44, 44, 44, 44, 44, 34, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 44, 44, 44, 44, 44, 44, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 745) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622550 none CO[C@@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 44, 44, 44, 44, 44, 44, 30, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 44, 44, 44, 44, 44, 44, 18, 18, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622550 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622550 Building ZINC000452622551 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622551 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/746 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622551 none CO[C@@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 47, 47, 47, 47, 47, 47, 47, 26, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 47, 47, 47, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/747 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/747' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622551 none CO[C@@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 48, 48, 48, 27, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622551 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 Building ZINC000452622551 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622551 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 746) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622551.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622551 none CO[C@@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 47, 47, 47, 47, 47, 47, 47, 26, 47, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 47, 47, 47, 47, 47, 47, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 747) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622551.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622551 none CO[C@@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 48, 48, 48, 27, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622551 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622551 Building ZINC000452622553 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622553 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/748 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622553 none CO[C@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 48, 48, 48, 26, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/749 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/749' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622553 none CO[C@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 48, 48, 48, 48, 48, 48, 48, 28, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 48, 48, 48, 48, 48, 48, 18, 18, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622553 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 Building ZINC000452622553 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622553 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 748) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622553 none CO[C@H]1COCC[C@@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [48, 48, 48, 48, 48, 48, 48, 48, 26, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 48, 48, 48, 48, 48, 48, 48, 48, 48, 16, 16, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 749) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622553 none CO[C@H]1COCC[C@@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [49, 48, 48, 48, 48, 48, 48, 48, 28, 48, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 49, 49, 49, 48, 48, 48, 48, 48, 48, 18, 18, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622553 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622553 Building ZINC000452622434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/750 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622434 none CO[C@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 44, 44, 44, 44, 44, 44, 30, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 44, 44, 44, 44, 44, 44, 18, 18, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/751 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/751' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622434 none CO[C@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 44, 44, 44, 44, 44, 44, 44, 34, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 44, 44, 44, 44, 44, 44, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 Building ZINC000452622434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452622434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 750) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452622434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622434 none CO[C@H]1COCC[C@H]1CNC(=O)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [46, 44, 44, 44, 44, 44, 44, 44, 30, 44, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 46, 46, 46, 44, 44, 44, 44, 44, 44, 18, 18, 3, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 751) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC000452622434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452622434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000452622434 none CO[C@H]1COCC[C@H]1CNC(=O)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [45, 44, 44, 44, 44, 44, 44, 44, 34, 44, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 45, 45, 45, 44, 44, 44, 44, 44, 44, 22, 22, 4, 3, 3, 6, 3, 3] 100 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/365617/xds-8058088.97/working/building/ZINC000452622434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452622434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452622434 Building ZINC000305663124 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305663124 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/752 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305663124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663124 none CC[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 14, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 6, 11, 11, 11, 11, 11, 14, 14, 15, 15, 45, 3, 6, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/753 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/753' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305663124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663124 none CC[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 13, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 11, 11, 11, 11, 11, 13, 13, 15, 15, 45, 3, 6, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305663124 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 Building ZINC000305663124 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305663124 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 752) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305663124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663124 none CC[C@@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 14, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 17, 6, 11, 11, 11, 11, 11, 14, 14, 15, 15, 45, 3, 6, 17, 17, 17, 17, 17, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 203 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 753) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305663124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663124 none CC[C@@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 13, 15, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 18, 6, 11, 11, 11, 11, 11, 13, 13, 15, 15, 45, 3, 6, 18, 18, 18, 18, 18, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 211 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305663124 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663124 Building ZINC000305663126 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305663126 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/754 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305663126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663126 none CC[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 12, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 16, 6, 11, 11, 11, 11, 11, 12, 12, 14, 14, 42, 3, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/755 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/755' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305663126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663126 none CC[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 3, 7, 7, 14, 15, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 18, 7, 12, 12, 12, 12, 12, 14, 14, 15, 15, 45, 3, 7, 18, 18, 18, 18, 18, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305663126 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 Building ZINC000305663126 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305663126 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 754) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663126.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305663126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663126 none CC[C@H](CCO)NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 3, 7, 7, 12, 14, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 16, 6, 11, 11, 11, 11, 11, 12, 12, 14, 14, 42, 3, 6, 16, 16, 16, 16, 16, 6] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 196 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 755) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305663126.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305663126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000305663126 none CC[C@H](CCO)NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 3, 7, 7, 14, 15, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 18, 7, 12, 12, 12, 12, 12, 14, 14, 15, 15, 45, 3, 7, 18, 18, 18, 18, 18, 7] 150 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 207 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305663126 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305663126 Building ZINC000305691408 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305691408 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/756 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO) `ZINC000305691408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305691408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305691408 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 12, 12, 33, 33, 33, 46, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 33, 33, 33, 46, 46, 138] 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]) total number of confs: 321 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/757 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/757' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO) `ZINC000305691408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305691408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305691408 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 11, 11, 33, 33, 33, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 33, 33, 33, 45, 45, 135] 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]) total number of confs: 323 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305691408 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 Building ZINC000305691408 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305691408 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 756) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO) `ZINC000305691408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305691408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305691408 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 12, 12, 33, 33, 33, 46, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 33, 33, 33, 46, 46, 138] 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]) total number of confs: 321 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 757) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO) `ZINC000305691408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305691408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000305691408 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)[C@H](C)CO NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 11, 11, 33, 33, 33, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 33, 33, 33, 45, 45, 135] 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]) total number of confs: 323 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305691408 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305691408 Building ZINC000305713858 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305713858 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/758 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305713858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713858 none CC[C@@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 12, 18, 20, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 18, 18, 18, 18, 18, 18, 20, 20, 60, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/759 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/759' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305713858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713858 none CC[C@@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 13, 17, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 17, 17, 17, 17, 17, 17, 19, 19, 57, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 211 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305713858 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 Building ZINC000305713858 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305713858 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 758) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305713858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713858 none CC[C@@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 12, 18, 20, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 18, 18, 18, 18, 18, 18, 20, 20, 60, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 759) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305713858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713858 none CC[C@@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 13, 17, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 17, 17, 17, 17, 17, 17, 19, 19, 57, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 211 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305713858 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713858 Building ZINC000305713861 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305713861 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/760 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305713861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713861 none CC[C@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 13, 17, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 17, 17, 17, 17, 17, 17, 17, 19, 19, 57, 10, 10, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/761 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/761' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305713861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713861 none CC[C@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 12, 18, 20, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 18, 18, 18, 18, 18, 18, 20, 20, 60, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305713861 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 Building ZINC000305713861 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305713861 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 760) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305713861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713861 none CC[C@H](CCO)CNC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 13, 17, 19, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 5, 17, 17, 17, 17, 17, 17, 17, 19, 19, 57, 10, 10, 2, 5, 11, 11, 11, 11, 11, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 208 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 761) grep: /scratch/xiaobo/365617/xds-8058088.97/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@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1) `ZINC000305713861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305713861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000305713861 none CC[C@H](CCO)CNC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 13, 10, 13, 12, 18, 20, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 12, 5, 17, 18, 18, 18, 18, 18, 18, 20, 20, 60, 10, 10, 2, 5, 12, 12, 12, 12, 12, 5] 150 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 235 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305713861 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305713861 Building ZINC000305717692 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305717692 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/762 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305717692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717692 none O=C(N1CC[C@@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 17, 17, 17, 17, 17, 31, 17, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 17, 31, 31, 93, 17, 17, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/763 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/763' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305717692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717692 none O=C(N1CC[C@@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 14, 27, 14, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 14, 14, 14, 14, 27, 27, 81, 14, 14, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305717692 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 Building ZINC000305717692 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305717692 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 762) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305717692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717692 none O=C(N1CC[C@@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 17, 17, 17, 17, 17, 31, 17, 1, 1, 1, 6, 6, 6, 6, 12, 12, 6, 12, 12, 6, 17, 17, 17, 17, 31, 31, 93, 17, 17, 6, 12, 12, 6, 12, 12, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 217 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 763) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305717692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717692 none O=C(N1CC[C@@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 14, 27, 14, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 14, 14, 14, 14, 27, 27, 81, 14, 14, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305717692 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717692 Building ZINC000305717693 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305717693 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/764 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305717693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717693 none O=C(N1CC[C@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 14, 27, 14, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 14, 14, 14, 14, 27, 27, 81, 14, 14, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/765 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/765' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305717693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717693 none O=C(N1CC[C@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 18, 18, 18, 18, 18, 32, 18, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 18, 18, 18, 18, 32, 32, 96, 18, 18, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305717693 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 Building ZINC000305717693 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305717693 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 764) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305717693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717693 none O=C(N1CC[C@H](CO)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 14, 14, 14, 14, 14, 27, 14, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 14, 14, 14, 14, 27, 27, 81, 14, 14, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 194 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 765) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305717693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305717693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000305717693 none O=C(N1CC[C@H](CO)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 5, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 7, 18, 18, 18, 18, 18, 32, 18, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 18, 18, 18, 18, 32, 32, 96, 18, 18, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [1, 10, 11, 12] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 223 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305717693 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305717693 Building ZINC000305725831 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305725831 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/766 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725831 none C[C@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 19, 31, 4, 8, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 19, 19, 19, 31, 31, 93, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/767 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/767' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725831 none C[C@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 16, 24, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 24, 24, 72, 7, 7, 7, 6, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305725831 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 Building ZINC000305725831 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305725831 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 766) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725831.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725831 none C[C@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 19, 19, 31, 4, 8, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 19, 19, 19, 31, 31, 93, 8, 8, 8, 6, 11, 11, 6, 11, 11, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 264 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 767) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725831.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305725831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725831 none C[C@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 16, 24, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 24, 24, 72, 7, 7, 7, 6, 14, 14, 14, 14, 14, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 220 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305725831 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725831 Building ZINC000305725833 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305725833 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/768 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305725833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725833 none C[C@@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 16, 24, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 24, 24, 72, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/769 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/769' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305725833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725833 none C[C@@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 21, 32, 4, 8, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 21, 21, 21, 32, 32, 96, 8, 8, 8, 6, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 277 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305725833 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 Building ZINC000305725833 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000305725833 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 768) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725833.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000305725833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725833 none C[C@@H](CO)N(C)C(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 16, 16, 24, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 14, 14, 6, 14, 14, 6, 16, 16, 16, 24, 24, 72, 7, 7, 7, 6, 14, 14, 6, 14, 14, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 206 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 769) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000305725833.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000305725833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000305725833 none C[C@@H](CO)N(C)C(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [21, 8, 21, 21, 32, 4, 8, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 6, 11, 11, 6, 21, 21, 21, 32, 32, 96, 8, 8, 8, 6, 11, 11, 11, 11, 11, 6] 150 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 277 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000305725833 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000305725833 Building ZINC000123050877 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123050877 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/770 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/770' -> `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)Nc1ccnn1C) `ZINC000123050877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123050877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000123050877 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 25, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/771 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/771' -> `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)Nc1ccnn1C) `ZINC000123050877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123050877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000123050877 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 27, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123050877 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 Building ZINC000123050877 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123050877 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 770) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C) `ZINC000123050877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123050877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000123050877 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 25, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 771) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C) `ZINC000123050877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123050877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000123050877 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.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, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 9, 27, 47, 47, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 27, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123050877 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123050877 Building ZINC000452745732 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452745732 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/772 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)n1) `ZINC000452745732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452745732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000452745732 none Cn1cc(Cl)c(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 16, 16, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/773 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/773' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(Cl)c(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1) `ZINC000452745732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452745732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000452745732 none Cn1cc(Cl)c(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 16, 16, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452745732 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 Building ZINC000452745732 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452745732 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 772) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc(Cl)c(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)n1) `ZINC000452745732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452745732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000452745732 none Cn1cc(Cl)c(CNC(=O)[C@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 16, 16, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 773) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc(Cl)c(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1) `ZINC000452745732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452745732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000452745732 none Cn1cc(Cl)c(CNC(=O)[C@@]([O-])([SiH3])c2cccn2C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 16, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 42, 42, 42, 42, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 42, 42, 42, 42, 42, 16, 16, 3, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452745732 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452745732 Building ZINC000531574045 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531574045 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/774 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000531574045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531574045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000531574045 none COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 14, 25, 25, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 35, 36, 36, 25, 25, 25, 25, 25, 25, 14, 14, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/775 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/775' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000531574045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531574045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000531574045 none COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 14, 25, 25, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 25, 25, 25, 25, 14, 14, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531574045 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 Building ZINC000531574045 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531574045 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 774) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000531574045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531574045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000531574045 none COC(C)(C)CN(C)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 14, 25, 25, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 35, 36, 36, 25, 25, 25, 25, 25, 25, 14, 14, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 132 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 775) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000531574045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531574045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000531574045 none COC(C)(C)CN(C)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 25, 14, 25, 25, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 36, 36, 36, 25, 25, 25, 25, 25, 25, 14, 14, 7, 7, 7, 6, 6, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 131 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531574045 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531574045 Building ZINC000123299006 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299006 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/776 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](O)C2)cn1) `ZINC000123299006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299006 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 4, 15, 15, 27, 27, 27, 27, 27, 27, 81, 27, 27, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/777 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](O)C2)cn1) `ZINC000123299006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299006 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 3, 14, 14, 35, 35, 35, 35, 35, 35, 105, 35, 35, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299006 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 Building ZINC000123299006 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299006 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 776) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](O)C2)cn1) `ZINC000123299006.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299006 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 15, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 4, 15, 15, 27, 27, 27, 27, 27, 27, 81, 27, 27, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 777) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](O)C2)cn1) `ZINC000123299006.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299006 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 35, 35, 35, 35, 35, 35, 35, 35, 6, 6, 6, 6, 6, 6, 3, 14, 14, 35, 35, 35, 35, 35, 35, 105, 35, 35, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299006 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299006 Building ZINC000123299228 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299228 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/778 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](O)C2)cn1) `ZINC000123299228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299228 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 2, 14, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/779 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/779' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](O)C2)cn1) `ZINC000123299228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299228 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 23, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 33, 33, 33, 99, 33, 33, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299228 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 Building ZINC000123299228 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299228 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 778) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](O)C2)cn1) `ZINC000123299228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299228 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 2, 14, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 779) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](O)C2)cn1) `ZINC000123299228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299228 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 23, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 33, 33, 33, 99, 33, 33, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299228 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299228 Building ZINC000123299478 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299478 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/780 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299478 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 23, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 33, 33, 33, 99, 33, 33, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/781 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299478 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 2, 14, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299478 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 Building ZINC000123299478 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299478 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 780) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299478 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 23, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 6, 6, 6, 6, 2, 14, 14, 33, 33, 33, 33, 33, 33, 99, 33, 33, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 781) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299478 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 22, 36, 36, 36, 36, 36, 36, 36, 36, 7, 7, 7, 7, 7, 7, 2, 14, 14, 36, 36, 36, 36, 36, 36, 108, 36, 36, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299478 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299478 Building ZINC000123299650 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299650 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/782 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299650 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 16, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 15, 15, 31, 31, 31, 31, 31, 31, 93, 31, 31, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/783 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/783' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299650 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 3, 16, 16, 31, 31, 31, 31, 31, 31, 93, 31, 31, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299650 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 Building ZINC000123299650 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000123299650 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 782) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000123299650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299650 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 16, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 4, 15, 15, 31, 31, 31, 31, 31, 31, 93, 31, 31, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 783) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](O)C2)cn1) `ZINC000123299650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000123299650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000123299650 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H]2CCC[C@@H](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.3', 'H', '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'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 5, 7, 12, 5, 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, 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: [7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 18, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7, 7, 7, 3, 16, 16, 31, 31, 31, 31, 31, 31, 93, 31, 31, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 198 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000123299650 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000123299650 Building ZINC000452880510 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452880510 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/784 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452880510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880510 none O=C(N1CCOC[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 21, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30, 5, 5] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 152 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/785 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452880510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880510 none O=C(N1CCOC[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 26, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 96, 32, 32, 7, 7] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452880510 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 Building ZINC000452880510 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452880510 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 784) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCOC[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880510.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452880510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880510 none O=C(N1CCOC[C@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [16, 2, 21, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 90, 30, 30, 5, 5] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 152 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 785) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCOC[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880510.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452880510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880510 none O=C(N1CCOC[C@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 2, 26, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 7, 7, 7, 7, 7, 32, 32, 32, 32, 32, 32, 96, 32, 32, 7, 7] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 163 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452880510 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880510 Building ZINC000452880511 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452880511 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/786 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452880511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880511 none O=C(N1CCOC[C@@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 20, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 84, 28, 28, 6, 6] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/787 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/787' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCOC[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452880511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880511 none O=C(N1CCOC[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 1, 22, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 93, 31, 31, 4, 4] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 155 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452880511 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 Building ZINC000452880511 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452880511 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 786) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCOC[C@@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452880511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880511 none O=C(N1CCOC[C@@H](O)C1)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [17, 2, 20, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 84, 28, 28, 6, 6] 150 rigid atoms, others: [11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 144 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 787) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCOC[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000452880511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452880511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC000452880511 none O=C(N1CCOC[C@@H](O)C1)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 7, 12, 5, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [18, 1, 22, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 93, 31, 31, 4, 4] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 155 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452880511 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452880511 Building ZINC000452885155 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452885155 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/788 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000452885155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452885155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000452885155 none CC(C)OC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 8, 17, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 22, 22, 26, 26, 26, 26, 26, 26, 26, 3, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/789 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000452885155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452885155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000452885155 none CC(C)OC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 27, 18, 8, 18, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 22, 22, 27, 27, 27, 27, 27, 27, 27, 3, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452885155 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 Building ZINC000452885155 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452885155 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 788) grep: /scratch/xiaobo/365617/xds-8058088.97/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)OC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000452885155.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452885155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000452885155 none CC(C)OC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 17, 8, 17, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 22, 22, 26, 26, 26, 26, 26, 26, 26, 3, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 789) grep: /scratch/xiaobo/365617/xds-8058088.97/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)OC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C) `ZINC000452885155.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452885155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000452885155 none CC(C)OC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 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, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 20, 27, 18, 8, 18, 3, 8, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 8, 22, 22, 27, 27, 27, 27, 27, 27, 27, 3, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 23] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452885155 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452885155 Building ZINC000452959177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452959177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/790 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452959177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959177 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 26, 26, 26, 11, 26, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 6, 5, 5, 2, 5, 5, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/791 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/791' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452959177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959177 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 1, 5, 5, 23, 23] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452959177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 Building ZINC000452959177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452959177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 790) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452959177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959177 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 26, 26, 26, 11, 26, 6, 1, 6, 1, 1, 1, 5, 5, 2, 5, 5, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 6, 5, 5, 2, 5, 5, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 791) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452959177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959177 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 1, 5, 5, 23, 23] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452959177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959177 Building ZINC000452959178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452959178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/792 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452959178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959178 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 2, 5, 5, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/793 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/793' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452959178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959178 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 39, 39, 39, 39, 39, 25, 25, 6, 5, 5, 1, 5, 5, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452959178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 Building ZINC000452959178 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452959178 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 792) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452959178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959178 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 23, 23, 23, 10, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 2, 5, 5, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 793) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O) `ZINC000452959178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452959178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000452959178 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 5, 5, 25, 25, 25, 39, 39, 39, 39, 39, 25, 25, 6, 5, 5, 1, 5, 5, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452959178 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452959178 Building ZINC000452968682 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452968682 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/794 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452968682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968682 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 40, 40, 40, 40, 40, 25, 25, 6, 5, 5, 10, 5, 5, 25, 25] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/795 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/795' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452968682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968682 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 5, 5, 5, 10, 5, 5, 26, 26] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452968682 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 Building ZINC000452968682 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452968682 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 794) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452968682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968682 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 40, 40, 40, 40, 40, 25, 25, 6, 5, 5, 10, 5, 5, 25, 25] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 795) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452968682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968682 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 5, 5, 5, 10, 5, 5, 26, 26] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452968682 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968682 Building ZINC000452968683 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452968683 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/796 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452968683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968683 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 5, 4, 4, 8, 4, 4, 26, 26] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/797 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/797' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452968683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968683 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 10, 5, 5, 23, 23] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452968683 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 Building ZINC000452968683 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452968683 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 796) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452968683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968683 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 5, 4, 4, 8, 4, 4, 26, 26] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 797) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O) `ZINC000452968683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452968683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452968683 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(O)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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: [40, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 23, 23, 23, 40, 40, 40, 40, 40, 23, 23, 6, 5, 5, 10, 5, 5, 23, 23] 100 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452968683 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452968683 Building ZINC000452971176 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452971176 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/798 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452971176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971176 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 26, 26, 26, 43, 43, 43, 43, 43, 26, 26, 5, 3, 3, 3, 3, 3, 3, 3, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/799 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/799' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452971176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971176 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 44, 44, 44, 44, 44, 23, 23, 6, 4, 4, 4, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452971176 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 Building ZINC000452971176 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452971176 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 798) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452971176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971176 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 26, 26, 26, 10, 26, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 26, 26, 26, 43, 43, 43, 43, 43, 26, 26, 5, 3, 3, 3, 3, 3, 3, 3, 26, 26] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 799) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452971176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971176 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 44, 44, 44, 44, 44, 23, 23, 6, 4, 4, 4, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452971176 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971176 Building ZINC000452971177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452971177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/800 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452971177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971177 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 23, 23, 23, 44, 44, 44, 44, 44, 23, 23, 6, 4, 4, 4, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/801 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/801' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452971177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971177 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 27, 27, 27, 10, 27, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 27, 27, 5, 3, 3, 3, 3, 3, 3, 3, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452971177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 Building ZINC000452971177 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452971177 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 800) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452971177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971177 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 23, 23, 23, 11, 23, 6, 1, 6, 1, 1, 1, 4, 4, 2, 4, 4, 4, 4, 23, 23, 23, 44, 44, 44, 44, 44, 23, 23, 6, 4, 4, 4, 4, 4, 4, 4, 23, 23] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 801) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O) `ZINC000452971177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452971177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000452971177 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccccc2OC)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.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'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 27, 27, 27, 10, 27, 5, 1, 5, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 27, 27, 27, 46, 46, 46, 46, 46, 27, 27, 5, 3, 3, 3, 3, 3, 3, 3, 27, 27] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452971177 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452971177 Building ZINC000452982067 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452982067 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/802 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452982067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982067 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 11, 26, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 6, 4, 4, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/803 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/803' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452982067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982067 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 41, 41, 41, 41, 41, 25, 25, 6, 5, 5, 5, 5, 5, 5, 5, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452982067 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 Building ZINC000452982067 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452982067 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 802) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452982067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982067 none CCN1C[C@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 11, 26, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 26, 26, 26, 40, 40, 40, 40, 40, 26, 26, 6, 4, 4, 4, 4, 4, 4, 4, 26, 26] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 803) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452982067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982067 none CCN1C[C@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 25, 25, 25, 41, 41, 41, 41, 41, 25, 25, 6, 5, 5, 5, 5, 5, 5, 5, 25, 25] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452982067 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982067 Building ZINC000452982071 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452982071 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/804 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452982071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982071 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 25, 25, 25, 41, 41, 41, 41, 41, 25, 25, 6, 5, 5, 5, 5, 5, 5, 5, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/805 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/805' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452982071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982071 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 41, 41, 41, 41, 41, 27, 27, 6, 5, 5, 5, 5, 5, 5, 5, 27, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452982071 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 Building ZINC000452982071 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452982071 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 804) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452982071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982071 none CCN1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 25, 25, 11, 25, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 25, 25, 25, 41, 41, 41, 41, 41, 25, 25, 6, 5, 5, 5, 5, 5, 5, 5, 25, 25] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 805) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O) `ZINC000452982071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452982071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000452982071 none CCN1C[C@@H](NC(=O)[C@]([O-])([SiH3])c2ccc(C)cc2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 5, 1, 1, 5, 1, 11, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 27, 27, 11, 27, 6, 1, 6, 1, 1, 1, 5, 5, 1, 1, 5, 5, 27, 27, 27, 41, 41, 41, 41, 41, 27, 27, 6, 5, 5, 5, 5, 5, 5, 5, 27, 27] 50 rigid atoms, others: [7, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452982071 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452982071 Building ZINC000452989276 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452989276 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/806 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452989276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452989276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452989276 none CO[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 10, 34, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 34, 34, 34, 34, 34, 34, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/807 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/807' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452989276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452989276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452989276 none CO[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 9, 35, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 45, 45, 45, 35, 35, 35, 35, 35, 35, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452989276 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 Building ZINC000452989276 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000452989276 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 806) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C) `ZINC000452989276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000452989276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452989276 none CO[C@@H]1CCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 34, 34, 34, 10, 34, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 43, 43, 43, 34, 34, 34, 34, 34, 34, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 105 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 807) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C) `ZINC000452989276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000452989276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000452989276 none CO[C@@H]1CCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1cccn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 35, 35, 35, 9, 35, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 45, 45, 45, 35, 35, 35, 35, 35, 35, 5, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000452989276 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000452989276 Building ZINC000531874037 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531874037 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/808 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1) `ZINC000531874037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531874037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874037 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 27, 26, 29, 26, 34, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 28, 87, 34, 34, 46, 46, 46, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 284 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/809 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/809' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1) `ZINC000531874037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531874037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874037 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 30, 25, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 12, 12, 30, 30, 90, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531874037 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 Building ZINC000531874037 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531874037 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 808) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1) `ZINC000531874037.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531874037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874037 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 27, 26, 29, 26, 34, 46, 46, 46, 46, 5, 5, 5, 5, 5, 5, 2, 12, 12, 29, 28, 87, 34, 34, 46, 46, 46, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 284 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 809) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1) `ZINC000531874037.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531874037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874037 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 27, 27, 30, 25, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 12, 12, 30, 30, 90, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 294 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531874037 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874037 Building ZINC000531874038 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531874038 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/810 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1) `ZINC000531874038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531874038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874038 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 30, 26, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 12, 12, 30, 30, 90, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/811 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/811' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1) `ZINC000531874038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531874038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874038 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 29, 26, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 11, 11, 29, 29, 87, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 283 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531874038 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 Building ZINC000531874038 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000531874038 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 810) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1) `ZINC000531874038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000531874038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874038 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 28, 28, 30, 26, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 12, 12, 30, 30, 90, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 285 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 811) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1) `ZINC000531874038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000531874038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000531874038 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@H](CO)Cc2ccco2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 11, 27, 27, 29, 26, 35, 47, 47, 47, 47, 5, 5, 5, 5, 5, 5, 2, 11, 11, 29, 29, 87, 35, 35, 47, 47, 47, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 283 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000531874038 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000531874038 Building ZINC000532008554 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532008554 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/812 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/812' -> `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)NCC1(C(=O)O)CCC1) `ZINC000532008554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532008554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000532008554 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 45, 46, 46, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 138, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/813 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/813' -> `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)NCC1(C(=O)O)CCC1) `ZINC000532008554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532008554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000532008554 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 27, 47, 48, 48, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 18, 18, 144, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 284 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000532008554 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 Building ZINC000532008554 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532008554 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 812) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1) `ZINC000532008554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532008554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000532008554 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 4, 4, 4, 30, 45, 46, 46, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 19, 19, 138, 45, 45, 45, 45, 45, 45] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 273 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 813) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1) `ZINC000532008554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532008554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000532008554 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(C(=O)O)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 11, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 6, 6, 6, 27, 47, 48, 48, 47, 47, 47, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 18, 18, 144, 47, 47, 47, 47, 47, 47] 150 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 284 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000532008554 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532008554 Building ZINC001142277594 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277594 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/814 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142277594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001142277594 none CNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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: [32, 32, 17, 32, 17, 17, 17, 5, 2, 9, 1, 1, 1, 5, 5, 5, 5, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 5, 5, 5, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/815 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/815' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142277594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001142277594 none CNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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: [38, 38, 15, 38, 15, 15, 15, 6, 2, 9, 1, 1, 1, 7, 7, 7, 7, 15, 15, 38, 38, 38, 38, 15, 15, 15, 15, 15, 7, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142277594 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 Building ZINC001142277594 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142277594 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 814) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142277594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142277594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001142277594 none CNC(=O)C1CCN(C(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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: [32, 32, 17, 32, 17, 17, 17, 5, 2, 9, 1, 1, 1, 5, 5, 5, 5, 17, 17, 32, 32, 32, 32, 17, 17, 17, 17, 17, 5, 5, 5, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 87 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 815) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142277594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142277594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001142277594 none CNC(=O)C1CCN(C(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 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: [38, 38, 15, 38, 15, 15, 15, 6, 2, 9, 1, 1, 1, 7, 7, 7, 7, 15, 15, 38, 38, 38, 38, 15, 15, 15, 15, 15, 7, 7, 7, 15, 15, 15, 15] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142277594 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142277594 Building ZINC001142278518 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278518 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/816 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ncn1) `ZINC001142278518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278518 none CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 28, 12, 12, 12, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 24, 12, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/817 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/817' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ncn1) `ZINC001142278518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278518 none CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 28, 12, 12, 12, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 24, 12, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278518 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 Building ZINC001142278518 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278518 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 816) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ncn1) `ZINC001142278518.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278518 none CC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 28, 12, 12, 12, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 24, 12, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 817) grep: /scratch/xiaobo/365617/xds-8058088.97/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(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ncn1) `ZINC001142278518.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278518 none CC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 1, 8, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 28, 12, 12, 12, 8, 8, 1, 8, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 28, 28, 28, 24, 12, 8, 12, 12, 12, 12] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278518 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278518 Building ZINC001142278593 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278593 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/818 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n2ncnc2n1) `ZINC001142278593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278593 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n2ncnc2n1 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', 'C.2', 'O.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 19, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 10, 10, 10, 25] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/819 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/819' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n2ncnc2n1) `ZINC001142278593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278593 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n2ncnc2n1 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', 'C.2', 'O.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 10, 10, 10, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278593 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 Building ZINC001142278593 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278593 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 818) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n2ncnc2n1) `ZINC001142278593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278593 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n2ncnc2n1 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', 'C.2', 'O.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 19, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 10, 10, 10, 25] 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]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 819) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n2ncnc2n1) `ZINC001142278593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278593 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n2ncnc2n1 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', 'C.2', 'O.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 12, 8, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 7, 1, 7, 1, 1, 1, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 19, 10, 10, 10, 26] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278593 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278593 Building ZINC000532237694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532237694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/820 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000532237694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532237694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000532237694 none COCC1(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 36, 36, 36, 31, 31, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/821 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/821' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000532237694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532237694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000532237694 none COCC1(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 11, 36, 36, 36, 32, 32, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 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]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000532237694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 Building ZINC000532237694 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000532237694 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 820) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000532237694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000532237694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000532237694 none COCC1(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 31, 12, 6, 6, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 12, 12, 36, 36, 36, 31, 31, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 123 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 821) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COCC1(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1) `ZINC000532237694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000532237694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000532237694 none COCC1(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 5, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 11, 11, 36, 36, 36, 32, 32, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11] 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]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000532237694 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000532237694 Building ZINC001142278745 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278745 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/822 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cncc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n1) `ZINC001142278745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278745 none COC(=O)c1cncc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 11, 32, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 11, 32, 32, 32, 11, 11, 6, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/823 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/823' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1cncc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n1) `ZINC001142278745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278745 none COC(=O)c1cncc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 11, 32, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 11, 32, 32, 32, 11, 11, 6, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278745 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 Building ZINC001142278745 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278745 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 822) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)c1cncc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n1) `ZINC001142278745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278745 none COC(=O)c1cncc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 11, 32, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 11, 32, 32, 32, 11, 11, 6, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 823) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)c1cncc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n1) `ZINC001142278745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 32 natoms 31 natoms 30 natoms 29 names: ZINC001142278745 none COC(=O)c1cncc(NC(=O)[C@]([O-])([SiH3])c2ccco2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 11, 32, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 11, 32, 32, 32, 11, 11, 6, 10, 10, 10] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278745 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278745 Building ZINC001142278787 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278787 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/824 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1C(N)=O) `ZINC001142278787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278787 none CSc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 10, 10, 10, 8, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 10, 10, 18, 18, 29, 29, 29, 8, 9, 9, 9, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/825 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/825' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1C(N)=O) `ZINC001142278787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278787 none CSc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 10, 10, 10, 8, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 10, 10, 18, 18, 29, 29, 29, 8, 9, 9, 9, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278787 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 Building ZINC001142278787 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142278787 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 824) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CSc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1C(N)=O) `ZINC001142278787.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142278787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278787 none CSc1n[nH]c(NC(=O)[C@@]([O-])([SiH3])c2ccco2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 10, 10, 10, 8, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 10, 10, 18, 18, 29, 29, 29, 8, 9, 9, 9, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 825) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CSc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1C(N)=O) `ZINC001142278787.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142278787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 33 natoms 32 natoms 31 natoms 30 names: ZINC001142278787 none CSc1n[nH]c(NC(=O)[C@]([O-])([SiH3])c2ccco2)c1C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 8, 6, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 10, 10, 10, 8, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 10, 10, 18, 18, 29, 29, 29, 8, 9, 9, 9, 18, 18] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 83 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142278787 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142278787 Building ZINC001142279407 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279407 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/826 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1n[nH]c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142279407 none COC(=O)c1n[nH]c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 32, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 32, 32, 32, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/827 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/827' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1n[nH]c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142279407 none COC(=O)c1n[nH]c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 32, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 32, 32, 32, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142279407 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 Building ZINC001142279407 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279407 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 826) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/826: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1n[nH]c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142279407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142279407 none COC(=O)c1n[nH]c(C)c1NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 32, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 32, 32, 32, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 827) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/827: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1n[nH]c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142279407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142279407 none COC(=O)c1n[nH]c(C)c1NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 8, 8, 6, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 32, 18, 18, 18, 18, 18, 18, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 32, 32, 32, 18, 18, 18, 4, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142279407 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142279407 Building ZINC001142282929 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282929 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/828 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C[C@@H]21) `ZINC001142282929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282929 none CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 38, 31, 6, 31, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/829 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C[C@@H]21) `ZINC001142282929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282929 none CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 32, 26, 6, 26, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 36, 36, 36, 36, 36, 6, 6, 5, 5, 5, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142282929 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 Building ZINC001142282929 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282929 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 828) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C[C@@H]21) `ZINC001142282929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282929 none CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c3ccco3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 38, 31, 6, 31, 6, 6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 6, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 829) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C[C@@H]21) `ZINC001142282929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001142282929 none CCOC(=O)[C@H]1[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c3ccco3)C[C@@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [36, 32, 26, 6, 26, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 36, 36, 36, 36, 36, 6, 6, 5, 5, 5, 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]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142282929 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282929 Building ZINC001142282829 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282829 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/830 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCO)CC(F)(F)F)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142282829 none O=C(N(CCO)CC(F)(F)F)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 21, 29, 10, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 21, 21, 29, 29, 87, 18, 18, 8, 8, 8] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 257 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/831 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/831' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(CCO)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142282829 none O=C(N(CCO)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 20, 28, 10, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 20, 20, 28, 28, 84, 18, 18, 9, 9, 9] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 249 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142282829 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 Building ZINC001142282829 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142282829 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 830) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N(CCO)CC(F)(F)F)[C@]([O-])([SiH3])c1ccco1) `ZINC001142282829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142282829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142282829 none O=C(N(CCO)CC(F)(F)F)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 21, 29, 10, 18, 18, 18, 18, 1, 1, 1, 8, 8, 8, 8, 21, 21, 29, 29, 87, 18, 18, 8, 8, 8] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 257 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 831) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N(CCO)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142282829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142282829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC001142282829 none O=C(N(CCO)CC(F)(F)F)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 12, 5, 5, 15, 15, 15, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 4, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 10, 20, 28, 10, 18, 18, 18, 18, 1, 1, 1, 9, 9, 9, 9, 20, 20, 28, 28, 84, 18, 18, 9, 9, 9] 150 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 249 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142282829 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142282829 Building ZINC001142283755 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283755 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/832 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142283755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142283755 none O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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: [11, 1, 8, 5, 5, 12, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 11, 11, 11, 11, 11, 33, 38, 38, 38, 38, 11, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 11, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 11, 11, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/833 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142283755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142283755 none O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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: [11, 1, 8, 5, 5, 12, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 11, 11, 11, 11, 11, 32, 40, 40, 40, 40, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142283755 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 Building ZINC001142283755 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283755 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 832) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142283755.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142283755 none O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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: [11, 1, 8, 5, 5, 12, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 11, 11, 11, 11, 11, 11, 33, 38, 38, 38, 38, 11, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 11, 27, 27, 38, 38, 38, 38, 38, 38, 38, 38, 11, 11, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 833) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142283755.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001142283755 none O=C(N1CCO[C@@H](CN2CCCC2)C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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: [11, 1, 8, 5, 5, 12, 5, 7, 5, 10, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 11, 11, 11, 11, 11, 11, 32, 40, 40, 40, 40, 11, 1, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 28, 28, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 6, 6, 6] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142283755 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283755 Building ZINC001142283039 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283039 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/834 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142283039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283039 none O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 10, 11, 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: [17, 2, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/835 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/835' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142283039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283039 none O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 10, 11, 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: [12, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142283039 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 Building ZINC001142283039 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142283039 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 834) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142283039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142283039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283039 none O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 10, 11, 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: [17, 2, 19, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 9, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 835) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142283039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142283039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142283039 none O=C(N1CCN2C(=O)CC[C@@H]2C1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 8, 10, 11, 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: [12, 2, 16, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142283039 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142283039 Building ZINC000428508914 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428508914 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/836 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428508914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508914 none C[C@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 11, 22, 29, 29, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 22, 22, 29, 29, 4, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/837 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/837' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428508914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508914 none C[C@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 24, 26, 26, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 24, 24, 26, 26, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428508914 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 Building ZINC000428508914 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428508914 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 836) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428508914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508914 none C[C@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 11, 22, 29, 29, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 9, 11, 11, 11, 22, 22, 29, 29, 4, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 837) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428508914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508914 none C[C@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 24, 26, 26, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 24, 24, 26, 26, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428508914 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508914 Building ZINC000428508916 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428508916 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/838 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428508916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508916 none C[C@@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 24, 26, 26, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 24, 24, 26, 26, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/839 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/839' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428508916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508916 none C[C@@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 11, 21, 28, 28, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 21, 21, 28, 28, 4, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428508916 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 Building ZINC000428508916 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000428508916 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 838) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/838: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508916.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000428508916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508916 none C[C@@H](CC(N)=O)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 4, 12, 12, 24, 26, 26, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 12, 24, 24, 26, 26, 4, 8, 8] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 839) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/839: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000428508916.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000428508916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000428508916 none C[C@@H](CC(N)=O)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 11, 11, 21, 28, 28, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 21, 21, 28, 28, 4, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000428508916 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000428508916 Building ZINC001142287453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/840 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C1CCOCC1) `ZINC001142287453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142287453 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 19, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 30, 30, 30, 30, 30, 19, 19, 19, 4, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/841 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/841' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C1CCOCC1) `ZINC001142287453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142287453 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 17, 3, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 32, 32, 32, 32, 32, 17, 17, 17, 3, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 Building ZINC001142287453 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287453 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 840) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C1CCOCC1) `ZINC001142287453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142287453 none COC(=O)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 10, 19, 4, 10, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 15, 30, 30, 30, 30, 30, 19, 19, 19, 4, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 841) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C1CCOCC1) `ZINC001142287453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142287453 none COC(=O)[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)C1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 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] 0 hydrogens 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, 9, 17, 3, 9, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 14, 32, 32, 32, 32, 32, 17, 17, 17, 3, 6, 6, 6, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287453 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287453 Building ZINC001142287648 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287648 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/842 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(=O)n1C) `ZINC001142287648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142287648 none CSc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 7, 7, 7, 6, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 12, 12, 37, 37, 37, 6, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/843 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(=O)n1C) `ZINC001142287648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142287648 none CSc1nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 7, 7, 7, 6, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 12, 12, 38, 38, 38, 6, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287648 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 Building ZINC001142287648 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287648 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 842) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CSc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(=O)n1C) `ZINC001142287648.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142287648 none CSc1nc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 7, 7, 7, 6, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 12, 12, 37, 37, 37, 6, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 843) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CSc1nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(=O)n1C) `ZINC001142287648.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001142287648 none CSc1nc(NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(=O)n1C NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 11, 8, 5, 7, 7, 7, 6, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 12, 12, 12, 12, 12, 38, 38, 38, 6, 10, 10, 10, 12, 12, 12, 12] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287648 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287648 Building ZINC001142287649 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287649 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/844 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287649 none CO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccco1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 12, 24, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 33, 33, 33, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/845 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287649 none CO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccco1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 26, 13, 26, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 34, 34, 34, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287649 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 Building ZINC001142287649 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142287649 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 844) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142287649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142287649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287649 none CO[C@@H]1COCC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccco1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 24, 24, 24, 24, 24, 24, 12, 24, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 33, 33, 33, 24, 24, 24, 24, 24, 24, 4, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 845) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142287649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142287649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142287649 none CO[C@@H]1COCC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccco1 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.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 12, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 26, 26, 26, 26, 26, 26, 13, 26, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 34, 34, 34, 26, 26, 26, 26, 26, 26, 6, 10, 10, 10] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142287649 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142287649 Building ZINC001142288130 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288130 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/846 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142288130 none CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 22, 11, 22, 4, 11, 11, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 23, 23, 69, 4, 8, 8, 8] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/847 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142288130 none CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 20, 12, 20, 4, 12, 12, 24, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 72, 4, 9, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 219 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288130 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 Building ZINC001142288130 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288130 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 846) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142288130 none CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 22, 11, 22, 4, 11, 11, 23, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 23, 23, 69, 4, 8, 8, 8] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 847) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142288130 none CC(C)(C)OC(=O)[C@H](CO)NC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 5, 7, 5, 12, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 25, 25, 20, 12, 20, 4, 12, 12, 24, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 72, 4, 9, 9, 9] 150 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 219 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288130 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288130 Building ZINC001142288238 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288238 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/848 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCCC2)COC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142288238 none O=C(NCC1(N2CCCC2)COC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 30, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 3, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 30, 30, 30, 30, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/849 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/849' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(N2CCCC2)COC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142288238 none O=C(NCC1(N2CCCC2)COC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 30, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 3, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 30, 30, 30, 30, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288238 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 Building ZINC001142288238 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288238 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 848) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCC1(N2CCCC2)COC1)[C@]([O-])([SiH3])c1ccco1) `ZINC001142288238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142288238 none O=C(NCC1(N2CCCC2)COC1)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 15, 30, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 3, 15, 15, 33, 33, 33, 33, 33, 33, 33, 33, 30, 30, 30, 30, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 114 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 849) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(NCC1(N2CCCC2)COC1)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142288238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001142288238 none O=C(NCC1(N2CCCC2)COC1)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 10, 5, 5, 5, 5, 5, 12, 5, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 16, 30, 33, 33, 33, 33, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 3, 16, 16, 33, 33, 33, 33, 33, 33, 33, 33, 30, 30, 30, 30, 8, 8, 8] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288238 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288238 Building ZINC001142288056 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288056 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/850 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288056 none CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 3, 8, 8, 8, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/851 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/851' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288056 none CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 23, 37, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 9, 9, 9, 37, 37] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288056 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 Building ZINC001142288056 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288056 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 850) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/850: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288056 none CN1C[C@@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 3, 8, 8, 8, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 851) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/851: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288056 none CN1C[C@@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 23, 37, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 14, 14, 4, 9, 9, 9, 37, 37] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288056 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288056 Building ZINC001142288057 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288057 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/852 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288057 none CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 22, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4, 9, 9, 9, 34, 34] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/853 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/853' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288057 none CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 3, 8, 8, 8, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288057 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 Building ZINC001142288057 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142288057 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 852) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288057.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142288057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288057 none CN1C[C@H](CNC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 22, 34, 4, 4, 1, 4, 1, 1, 1, 9, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 14, 14, 4, 9, 9, 9, 34, 34] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 853) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O) `ZINC001142288057.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142288057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC001142288057 none CN1C[C@H](CNC(=O)[C@]([O-])([SiH3])c2ccco2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 27, 43, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 3, 8, 8, 8, 43, 43] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142288057 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142288057 Building ZINC001142291415 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291415 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/854 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/855 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/855' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/856 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/856' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/857 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/857' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291415 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 Building ZINC001142291415 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291415 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 854) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 855) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 856) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 857) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291415 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 Building ZINC001142291415 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291415 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 854) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 855) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 856) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 857) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291415 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 Building ZINC001142291415 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001142291415 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 854) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/854: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 855) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/855: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 29, 9, 2, 2, 1, 2, 1, 1, 1, 7, 7, 7, 7, 40, 40, 40, 40, 40, 40, 40, 40, 40, 14, 14, 9, 9, 2, 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]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 856) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/856: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 857) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/857: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291415.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001142291415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC001142291415 none C[C@@H]1COCCN1CCNC(=O)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 12, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 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, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 33, 11, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 16, 16, 11, 11, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291415 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291415 Building ZINC001142291097 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291097 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/858 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2n(n1)CCCO2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142291097 none O=C(NCc1cc2n(n1)CCCO2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 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: [3, 1, 3, 3, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 3, 14, 14, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/859 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/859' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2n(n1)CCCO2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142291097 none O=C(NCc1cc2n(n1)CCCO2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 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: [3, 1, 3, 3, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 3, 14, 14, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291097 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 Building ZINC001142291097 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291097 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 858) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/858: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2n(n1)CCCO2)[C@]([O-])([SiH3])c1ccco1) `ZINC001142291097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142291097 none O=C(NCc1cc2n(n1)CCCO2)[C@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 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: [3, 1, 3, 3, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 3, 14, 14, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 859) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/859: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1cc2n(n1)CCCO2)[C@@]([O-])([SiH3])c1ccco1) `ZINC001142291097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001142291097 none O=C(NCc1cc2n(n1)CCCO2)[C@@]([O-])([SiH3])c1ccco1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 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: [3, 1, 3, 3, 14, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1, 6, 6, 6, 6, 3, 14, 14, 39, 39, 39, 39, 39, 39, 39, 6, 6, 6] 50 rigid atoms, others: [1, 13, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC001142291097 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC001142291097 Building ZINC000170926148 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170926148 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/860 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc(CO)c2)cn1) `ZINC000170926148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170926148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000170926148 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc(CO)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', 'O.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 36, 36, 36, 36, 36, 38, 34, 5, 5, 5, 5, 5, 5, 2, 12, 12, 36, 36, 36, 38, 38, 114, 36, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/861 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/861' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc(CO)c2)cn1) `ZINC000170926148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170926148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000170926148 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc(CO)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', 'O.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 36, 36, 36, 36, 36, 39, 33, 5, 5, 5, 5, 5, 5, 2, 12, 12, 36, 36, 36, 39, 39, 117, 36, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000170926148 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 Building ZINC000170926148 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000170926148 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 860) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc(CO)c2)cn1) `ZINC000170926148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000170926148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000170926148 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2cccc(CO)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', 'O.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 36, 36, 36, 36, 36, 38, 34, 5, 5, 5, 5, 5, 5, 2, 12, 12, 36, 36, 36, 38, 38, 114, 36, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 212 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 861) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc(CO)c2)cn1) `ZINC000170926148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000170926148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000170926148 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2cccc(CO)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', 'O.3', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 12, 36, 36, 36, 36, 36, 39, 33, 5, 5, 5, 5, 5, 5, 2, 12, 12, 36, 36, 36, 39, 39, 117, 36, 5] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000170926148 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000170926148 Building ZINC000171263383 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171263383 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/862 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171263383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263383 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 25, 45, 45, 25, 25, 25, 7, 6, 6, 6, 6, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/863 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/863' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171263383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263383 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 22, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 46, 46, 22, 22, 22, 6, 6, 6, 6, 6, 46, 46] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171263383 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 Building ZINC000171263383 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171263383 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 862) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171263383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263383 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 25, 45, 45, 25, 25, 25, 7, 6, 6, 6, 6, 45, 45] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 863) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171263383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263383 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 22, 6, 1, 6, 1, 1, 1, 6, 6, 1, 1, 6, 6, 22, 46, 46, 22, 22, 22, 6, 6, 6, 6, 6, 46, 46] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171263383 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263383 Building ZINC000171263388 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171263388 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/864 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171263388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263388 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 22, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 22, 46, 46, 22, 22, 22, 6, 6, 6, 6, 6, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/865 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/865' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171263388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263388 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 45, 45, 25, 25, 25, 7, 6, 6, 6, 6, 45, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171263388 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 Building ZINC000171263388 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171263388 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 864) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263388.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171263388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263388 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 22, 6, 1, 6, 1, 1, 1, 6, 6, 1, 6, 6, 6, 22, 46, 46, 22, 22, 22, 6, 6, 6, 6, 6, 46, 46] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 172 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 865) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O) `ZINC000171263388.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171263388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000171263388 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 25, 7, 1, 7, 1, 1, 1, 6, 6, 1, 1, 6, 6, 25, 45, 45, 25, 25, 25, 7, 6, 6, 6, 6, 45, 45] 50 rigid atoms, others: [4, 6, 7, 8] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171263388 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171263388 Building ZINC000171454147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171454147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/866 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1) `ZINC000171454147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171454147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454147 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 15, 15, 15, 19, 31, 31, 31, 30, 15, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 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: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/867 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/867' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1) `ZINC000171454147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171454147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454147 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 21, 31, 31, 31, 31, 16, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171454147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 Building ZINC000171454147 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171454147 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 866) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1) `ZINC000171454147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171454147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454147 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 15, 15, 15, 15, 19, 31, 31, 31, 30, 15, 8, 8, 8, 8, 8, 8, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 15, 15, 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: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 867) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1) `ZINC000171454147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171454147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454147 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 6, 16, 16, 16, 16, 21, 31, 31, 31, 31, 16, 7, 7, 7, 7, 7, 7, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171454147 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454147 Building ZINC000171454153 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171454153 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/868 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1) `ZINC000171454153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171454153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454153 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 6, 17, 17, 17, 17, 21, 30, 30, 30, 30, 17, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/869 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/869' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1) `ZINC000171454153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171454153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454153 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 16, 16, 16, 16, 20, 31, 31, 31, 30, 16, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 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: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171454153 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 Building ZINC000171454153 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171454153 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 868) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1) `ZINC000171454153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171454153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454153 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 4, 6, 17, 17, 17, 17, 21, 30, 30, 30, 30, 17, 7, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 17, 17, 7] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 869) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1) `ZINC000171454153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171454153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC000171454153 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@H](N3CCCC3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 10, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 16, 16, 16, 16, 20, 31, 31, 31, 30, 16, 8, 8, 8, 8, 8, 8, 16, 16, 16, 16, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 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: 65 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171454153 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171454153 Building ZINC000171573906 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171573906 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/870 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000171573906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171573906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000171573906 none Cc1cccnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 16, 16, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/871 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/871' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000171573906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171573906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000171573906 none Cc1cccnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 15, 15, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171573906 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 Building ZINC000171573906 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000171573906 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 870) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1cccnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000171573906.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000171573906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000171573906 none Cc1cccnc1CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 16, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 16, 16, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 871) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1cccnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000171573906.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000171573906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000171573906 none Cc1cccnc1CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 15, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 30, 30, 15, 15, 4, 8, 8, 8, 8, 8] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000171573906 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000171573906 Building ZINC000172635902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172635902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/872 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172635902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635902 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 29, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 34, 34, 34, 29, 29, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/873 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/873' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172635902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635902 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 31, 31, 31, 30, 30, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172635902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 Building ZINC000172635902 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172635902 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 872) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635902.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172635902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635902 none COC[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 29, 13, 13, 13, 13, 7, 1, 7, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 34, 34, 34, 29, 29, 13, 13, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 873) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635902.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172635902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635902 none COC[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 10, 10, 10, 10, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 31, 31, 31, 30, 30, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172635902 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635902 Building ZINC000172635909 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172635909 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/874 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172635909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635909 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 31, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 34, 34, 34, 31, 31, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/875 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/875' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172635909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635909 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 29, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 32, 32, 32, 29, 29, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172635909 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 Building ZINC000172635909 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172635909 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 874) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635909.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172635909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635909 none COC[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 31, 11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 34, 34, 34, 31, 31, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 875) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1) `ZINC000172635909.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172635909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000172635909 none COC[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)CCO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [32, 29, 11, 11, 11, 11, 6, 1, 6, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 32, 32, 32, 29, 29, 11, 11, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172635909 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172635909 Building ZINC000172648202 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172648202 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/876 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172648202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648202 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 39, 16, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 28, 38, 38, 35, 39, 39, 39, 16, 16, 3, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/877 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/877' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172648202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648202 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 26, 44, 12, 26, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 26, 26, 26, 26, 44, 44, 44, 12, 12, 2, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 178 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172648202 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 Building ZINC000172648202 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172648202 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 876) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648202.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172648202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648202 none COC(=O)[C@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 39, 16, 31, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 28, 38, 38, 35, 39, 39, 39, 16, 16, 3, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 877) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648202.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172648202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648202 none COC(=O)[C@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 26, 44, 12, 26, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 26, 26, 26, 26, 44, 44, 44, 12, 12, 2, 5, 5, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 178 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172648202 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648202 Building ZINC000172648208 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172648208 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/878 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172648208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648208 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 35, 40, 16, 35, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 32, 40, 40, 37, 40, 40, 40, 16, 16, 3, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 235 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/879 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/879' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172648208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648208 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 43, 13, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 27, 27, 27, 43, 43, 43, 13, 13, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172648208 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 Building ZINC000172648208 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172648208 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 878) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172648208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648208 none COC(=O)[C@@H](CNC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 35, 40, 16, 35, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 32, 40, 40, 37, 40, 40, 40, 16, 16, 3, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 235 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 879) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C) `ZINC000172648208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172648208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000172648208 none COC(=O)[C@@H](CNC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.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'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 43, 13, 27, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 27, 27, 27, 27, 43, 43, 43, 13, 13, 2, 5, 5, 5, 5, 5, 27, 27, 27, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 172 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172648208 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172648208 Building ZINC000172589161 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172589161 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/880 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000172589161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172589161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000172589161 none NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 36, 36, 26, 26, 6, 4, 4, 4, 4] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/881 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/881' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000172589161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172589161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000172589161 none NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 36, 36, 26, 26, 6, 4, 4, 4, 4] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172589161 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 Building ZINC000172589161 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000172589161 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 880) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000172589161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000172589161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000172589161 none NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 36, 36, 26, 26, 6, 4, 4, 4, 4] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 881) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC000172589161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000172589161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000172589161 none NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 45, 26, 6, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 45, 45, 36, 36, 26, 26, 6, 4, 4, 4, 4] 50 rigid atoms, others: [6, 8, 9, 10] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000172589161 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000172589161 Building ZINC000174144716 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174144716 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/882 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000174144716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174144716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000174144716 none COC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 31, 31, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/883 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/883' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000174144716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174144716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000174144716 none COC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 28, 10, 26, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 28, 28, 28, 28, 28, 28, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000174144716 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 Building ZINC000174144716 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174144716 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 882) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000174144716.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174144716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000174144716 none COC(C)(C)CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 31, 31, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 883) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000174144716.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174144716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000174144716 none COC(C)(C)CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 28, 10, 26, 27, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 32, 32, 32, 28, 28, 28, 28, 28, 28, 10, 10, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 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: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000174144716 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174144716 Building ZINC000174587361 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587361 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/884 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000174587361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000174587361 none O=C(N1CC[C@@H](O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 22, 22, 9, 22, 22, 9, 20, 20, 20, 20, 60, 20, 20, 9, 22, 22, 14, 22, 22, 9] 150 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/885 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/885' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CC[C@@H](O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000174587361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000174587361 none O=C(N1CC[C@@H](O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 7, 16, 16, 16, 16, 16, 16, 1, 1, 1, 10, 10, 10, 10, 20, 20, 14, 20, 20, 10, 16, 16, 16, 16, 48, 16, 16, 10, 20, 20, 20, 20, 20, 10] 150 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000174587361 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 Building ZINC000174587361 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000174587361 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 884) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@@H](O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000174587361.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000174587361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000174587361 none O=C(N1CC[C@@H](O)C1)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 8, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 22, 22, 9, 22, 22, 9, 20, 20, 20, 20, 60, 20, 20, 9, 22, 22, 14, 22, 22, 9] 150 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 885) grep: /scratch/xiaobo/365617/xds-8058088.97/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: O=C(N1CC[C@@H](O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000174587361.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000174587361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000174587361 none O=C(N1CC[C@@H](O)C1)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 7, 12, 5, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 4, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 7, 16, 16, 16, 16, 16, 16, 1, 1, 1, 10, 10, 10, 10, 20, 20, 14, 20, 20, 10, 16, 16, 16, 16, 48, 16, 16, 10, 20, 20, 20, 20, 20, 10] 150 rigid atoms, others: [1, 10, 11, 9] set([0, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000174587361 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000174587361 Building ZINC000175431609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175431609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/886 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000175431609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175431609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000175431609 none NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 28, 28, 19, 19, 13, 13, 4, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/887 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000175431609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175431609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000175431609 none NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 29, 29, 20, 20, 13, 13, 4, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175431609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 Building ZINC000175431609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175431609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 886) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000175431609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175431609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000175431609 none NC(=O)CCNC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 28, 28, 19, 19, 13, 13, 4, 6, 10, 10, 6, 10, 10, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 887) grep: /scratch/xiaobo/365617/xds-8058088.97/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: NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000175431609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175431609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000175431609 none NC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 20, 29, 13, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 6, 10, 10, 6, 29, 29, 20, 20, 13, 13, 4, 6, 10, 10, 10, 10, 10, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175431609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175431609 Building ZINC000175813385 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175813385 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/888 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175813385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 11, 22, 23, 23, 25, 27, 27, 11, 11, 11, 5, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 25, 25, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/889 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/889' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175813385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 24, 23, 24, 26, 28, 28, 11, 11, 11, 5, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 26, 26, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175813385 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 Building ZINC000175813385 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175813385 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 888) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175813385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813385 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 10, 10, 10, 10, 10, 11, 22, 23, 23, 25, 27, 27, 11, 11, 11, 5, 10, 10, 10, 10, 10, 23, 23, 23, 23, 23, 23, 25, 25, 27, 27, 27, 27, 27, 27] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 889) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175813385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813385 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 5, 11, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 11, 24, 23, 24, 26, 28, 28, 11, 11, 11, 5, 11, 11, 11, 11, 11, 24, 24, 24, 24, 24, 24, 26, 26, 28, 28, 28, 28, 28, 28] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 134 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175813385 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813385 Building ZINC000175813406 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175813406 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/890 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175813406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813406 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 26, 26, 12, 12, 12, 5, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/891 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/891' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175813406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813406 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 25, 25, 25, 25, 26, 26, 12, 12, 12, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175813406 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 Building ZINC000175813406 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000175813406 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 890) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813406.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000175813406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813406 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 12, 12, 12, 12, 12, 12, 24, 24, 24, 24, 26, 26, 12, 12, 12, 5, 12, 12, 12, 12, 12, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 118 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 891) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C) `ZINC000175813406.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000175813406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC000175813406 none C[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(C)c1)C(C)(C)CN(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 5, 5, 10, 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] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 12, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 25, 25, 25, 25, 26, 26, 12, 12, 12, 5, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 116 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000175813406 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000175813406 Building ZINC000760154844 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760154844 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/892 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1) `ZINC000760154844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760154844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000760154844 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 25, 4, 4, 9, 9, 26, 26, 26, 26, 26, 9, 4, 25, 25, 25, 25, 25, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/893 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/893' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1) `ZINC000760154844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760154844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000760154844 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 27, 27, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 4, 27, 27, 27, 27, 27, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760154844 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 Building ZINC000760154844 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000760154844 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 892) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/892: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1) `ZINC000760154844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760154844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000760154844 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 25, 25, 4, 4, 9, 9, 26, 26, 26, 26, 26, 9, 4, 25, 25, 25, 25, 25, 9] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 893) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/893: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1) `ZINC000760154844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760154844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC000760154844 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2nc(C3CC3)no2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 5, 5, 5, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 27, 27, 4, 4, 7, 7, 26, 26, 26, 26, 26, 7, 4, 27, 27, 27, 27, 27, 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]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760154844 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760154844 Building ZINC000760157283 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157283 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/894 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/895 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/895' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/896 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/896' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/897 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/897' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157283 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 Building ZINC000760157283 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157283 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 894) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 895) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 896) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 897) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157283 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 Building ZINC000760157283 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157283 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 894) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 895) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 896) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 897) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157283 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 Building ZINC000760157283 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157283 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 894) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/894: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 895) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/895: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 896) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/896: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 4, 9, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 17, 17, 17, 17, 17, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 897) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1) `ZINC000760157283.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157283 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 10, 10, 10, 10, 10, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157283 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157283 Building ZINC000760157285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/898 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/899 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/899' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/900 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/900' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/901 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/901' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 Building ZINC000760157285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 898) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 899) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 900) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 901) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 Building ZINC000760157285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 898) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 899) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 900) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 901) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 Building ZINC000760157285 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000760157285 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 898) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 899) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 900) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 5, 5, 5, 1, 1, 1, 1, 6, 10, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 17, 17, 17, 17, 17, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 901) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1) `ZINC000760157285.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000760157285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000760157285 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCN(C)[C@H](C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 7, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 14, 14, 14, 14, 14, 4, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000760157285 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000760157285 Building ZINC000176775115 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176775115 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/902 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1) `ZINC000176775115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176775115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775115 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 31, 31, 31, 9, 9, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/903 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/903' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1) `ZINC000176775115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176775115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775115 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 10, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 29, 29, 29, 10, 10, 3] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000176775115 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 Building ZINC000176775115 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176775115 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 902) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1) `ZINC000176775115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176775115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775115 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 31, 31, 31, 9, 9, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 903) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1) `ZINC000176775115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176775115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775115 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 10, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 29, 29, 29, 10, 10, 3] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000176775115 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775115 Building ZINC000176775129 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176775129 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/904 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1) `ZINC000176775129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176775129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775129 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 10, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 29, 29, 29, 10, 10, 3] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/905 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/905' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1) `ZINC000176775129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176775129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775129 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 31, 31, 31, 9, 9, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000176775129 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 Building ZINC000176775129 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000176775129 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 904) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1) `ZINC000176775129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000176775129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775129 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [3, 3, 3, 1, 1, 1, 2, 5, 6, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 10, 3, 3, 3, 3, 3, 3, 10, 10, 10, 10, 29, 29, 29, 10, 10, 3] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 905) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1) `ZINC000176775129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000176775129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000176775129 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCO[C@@H](c3ccco3)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 7, 1, 1, 1, 1, 12, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [4, 4, 4, 1, 1, 1, 2, 5, 6, 9, 9, 9, 9, 9, 9, 31, 31, 31, 31, 9, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 31, 31, 31, 9, 9, 4] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000176775129 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000176775129 Building ZINC000177235739 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177235739 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/906 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1) `ZINC000177235739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177235739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000177235739 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 3, 14, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/907 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/907' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1) `ZINC000177235739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177235739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000177235739 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 3, 14, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177235739 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 Building ZINC000177235739 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177235739 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 906) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1) `ZINC000177235739.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177235739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000177235739 none Cn1cc([C@@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 3, 14, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 907) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1) `ZINC000177235739.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177235739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 35 natoms 34 natoms 33 natoms 32 names: ZINC000177235739 none Cn1cc([C@]([O-])([SiH3])C(=O)N2CCOc3ncccc32)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 1, 1, 1, 3, 14, 20, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 11, 11, 23, 23, 23, 23, 23, 23, 23, 11] 44 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177235739 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177235739 Building ZINC000177245434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177245434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/908 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/908' -> `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)Nc1cnn(C)c1C) `ZINC000177245434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177245434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000177245434 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 24, 24, 24, 24, 24, 24, 24] 28 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/909 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/909' -> `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)Nc1cnn(C)c1C) `ZINC000177245434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177245434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000177245434 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 25, 25, 25, 25, 25, 25, 25] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177245434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 Building ZINC000177245434 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000177245434 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 908) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C) `ZINC000177245434.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177245434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000177245434 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 9, 9, 9, 24, 24, 24, 24, 24, 24, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 24, 24, 24, 24, 24, 24, 24] 28 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 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: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 909) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C) `ZINC000177245434.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177245434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000177245434 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 25, 25, 25, 25, 25, 25, 25] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177245434 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177245434 Building ZINC000177759387 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000177759387 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/910 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/911 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/911' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/912 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/912' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/913 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/913' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177759387 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 Building ZINC000177759387 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000177759387 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 910) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 911) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 912) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 913) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177759387 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 Building ZINC000177759387 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000177759387 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 910) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 911) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 912) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 913) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177759387 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 Building ZINC000177759387 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000177759387 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 910) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 911) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 1, 10, 1, 1, 1, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 102 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `2' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 2 (index: 912) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `3' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 3 (index: 913) grep: /scratch/xiaobo/365617/xds-8058088.97/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC000177759387.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000177759387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000177759387 none CCN1CC[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 9, 1, 1, 1, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000177759387 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/0.* 3: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/3.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/1.* 2: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387/2.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000177759387 Building ZINC000178064292 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178064292 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/914 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1) `ZINC000178064292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178064292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178064292 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/915 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/915' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1) `ZINC000178064292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178064292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178064292 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178064292 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 Building ZINC000178064292 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178064292 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 914) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1) `ZINC000178064292.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178064292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178064292 none Cn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 915) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1) `ZINC000178064292.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178064292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000178064292 none Cn1cc([C@]([O-])([SiH3])C(=O)NCc2ccn3ccnc3c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 13, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 13, 13, 32, 32, 32, 32, 32, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178064292 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178064292 Building ZINC000178307584 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307584 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/916 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307584 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 10, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 2, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/917 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/917' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307584 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307584 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 Building ZINC000178307584 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307584 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 916) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307584 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 10, 31, 31, 31, 31, 31, 31, 31, 31, 8, 8, 8, 8, 8, 8, 2, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 917) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307584 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 32, 32, 32, 32, 32, 32, 32, 32, 6, 6, 6, 6, 6, 6, 2, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307584 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307584 Building ZINC000178307595 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307595 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/918 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307595 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 3, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/919 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/919' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307595 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 2, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307595 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 Building ZINC000178307595 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307595 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 918) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307595.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307595 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 15, 27, 27, 27, 27, 27, 27, 27, 27, 8, 8, 8, 8, 8, 8, 3, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 81, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 919) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1) `ZINC000178307595.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307595 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 18, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 2, 11, 11, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307595 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307595 Building ZINC000178307609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/920 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307609 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 5, 21, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 5, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 99, 11] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/921 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/921' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307609 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 22, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 10, 10, 5, 19, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 Building ZINC000178307609 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307609 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 920) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307609 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 11, 1, 1, 1, 1, 5, 5, 5, 21, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 11, 11, 11, 5, 18, 18, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 99, 11] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 215 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 921) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307609 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 22, 32, 32, 32, 32, 32, 32, 32, 32, 10, 10, 10, 10, 10, 10, 5, 19, 19, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 96, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307609 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307609 Building ZINC000178307620 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307620 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/922 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307620 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/923 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/923' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307620 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 10, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 2, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307620 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 Building ZINC000178307620 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178307620 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 922) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178307620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307620 none Cn1cc([C@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 11, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 2, 11, 11, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 93, 6] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 923) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1) `ZINC000178307620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178307620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000178307620 none Cn1cc([C@@]([O-])([SiH3])C(=O)NC[C@]2(C)CCCC[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 10, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 7, 7, 7, 7, 2, 10, 10, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 87, 7] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178307620 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178307620 Building ZINC000178710229 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178710229 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/924 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000178710229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178710229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000178710229 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 78, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/925 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/925' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000178710229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178710229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000178710229 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 5, 27, 27, 27, 27, 27, 27, 81, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178710229 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 Building ZINC000178710229 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000178710229 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 924) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000178710229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000178710229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000178710229 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 10, 5, 26, 26, 26, 26, 26, 26, 78, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 925) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000178710229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000178710229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000178710229 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 10, 1, 1, 1, 1, 5, 5, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 10, 10, 5, 27, 27, 27, 27, 27, 27, 81, 10] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000178710229 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000178710229 Building ZINC000429728001 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429728001 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/926 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429728001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429728001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000429728001 none CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 22, 17, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 31, 22, 22, 17, 17, 4, 8, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/927 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/927' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429728001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429728001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000429728001 none CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 22, 18, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 22, 22, 18, 18, 4, 8, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000429728001 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 Building ZINC000429728001 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000429728001 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 926) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429728001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000429728001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000429728001 none CC(=O)NCCNC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 22, 17, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 31, 31, 31, 31, 22, 22, 17, 17, 4, 8, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 927) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1) `ZINC000429728001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000429728001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 31 natoms 30 natoms 29 natoms 28 names: ZINC000429728001 none CC(=O)NCCNC(=O)[C@]([O-])([SiH3])c1ccc(Cl)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 22, 18, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 22, 22, 18, 18, 4, 8, 8] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000429728001 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000429728001 Building ZINC000179377859 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179377859 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/928 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000179377859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179377859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179377859 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 6, 3, 12, 12, 12, 12, 12, 12, 36, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/929 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/929' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000179377859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179377859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179377859 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 13, 13, 13, 13, 13, 6, 4, 15, 15, 15, 15, 15, 15, 45, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179377859 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 Building ZINC000179377859 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179377859 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 928) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000179377859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179377859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179377859 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 6, 6, 1, 1, 1, 1, 3, 3, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 6, 14, 14, 14, 14, 14, 6, 3, 12, 12, 12, 12, 12, 12, 36, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 929) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1) `ZINC000179377859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179377859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179377859 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@H]2Cc3ccccc3[C@H]2O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [13, 6, 6, 6, 1, 1, 1, 1, 4, 4, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 6, 13, 13, 13, 13, 13, 6, 4, 15, 15, 15, 15, 15, 15, 45, 6] 150 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179377859 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179377859 Building ZINC000179131820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179131820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/930 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1) `ZINC000179131820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179131820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131820 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 22, 22, 22, 6, 4, 4, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/931 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/931' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1) `ZINC000179131820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179131820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131820 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 20, 20, 5, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179131820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 Building ZINC000179131820 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179131820 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 930) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1) `ZINC000179131820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179131820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131820 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 3, 6, 6, 6, 6, 6, 22, 22, 22, 6, 4, 4, 14, 14, 14, 14, 14, 4, 6, 6, 6, 6, 6, 6, 6, 22, 22, 22, 6, 6, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 931) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1) `ZINC000179131820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179131820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131820 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 20, 20, 5, 4, 4, 11, 11, 11, 11, 11, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179131820 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131820 Building ZINC000179131829 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179131829 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/932 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1) `ZINC000179131829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179131829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131829 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 20, 20, 5, 4, 4, 14, 14, 14, 14, 14, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/933 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/933' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1) `ZINC000179131829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179131829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131829 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 19, 19, 19, 5, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179131829 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 Building ZINC000179131829 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179131829 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 932) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1) `ZINC000179131829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179131829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131829 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 20, 20, 20, 5, 4, 4, 14, 14, 14, 14, 14, 4, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 933) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1) `ZINC000179131829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179131829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC000179131829 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CC[C@](C)(C(=O)OC)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 11, 12, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 2, 3, 5, 5, 5, 5, 5, 19, 19, 19, 5, 4, 4, 16, 16, 16, 16, 16, 4, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 5, 5, 4] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179131829 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179131829 Building ZINC000179190608 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179190608 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/934 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1) `ZINC000179190608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179190608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179190608 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 14, 14, 19, 21, 21, 21, 6, 6, 15, 15, 15, 15, 15, 6, 2, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/935 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/935' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1) `ZINC000179190608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179190608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179190608 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 11, 11, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179190608 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 Building ZINC000179190608 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179190608 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 934) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1) `ZINC000179190608.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179190608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179190608 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 14, 14, 19, 21, 21, 21, 6, 6, 15, 15, 15, 15, 15, 6, 2, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 935) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1) `ZINC000179190608.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179190608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000179190608 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@H](C)C(=O)OC(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 11, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 11, 11, 15, 15, 15, 15, 6, 6, 15, 15, 15, 15, 15, 6, 3, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179190608 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179190608 Building ZINC000179449600 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449600 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/936 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449600 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 16, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 20, 20, 20, 20, 20, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/937 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/937' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449600 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 7, 15, 14, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 17, 17, 17, 17, 17, 15, 15, 15, 2, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449600 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 Building ZINC000179449600 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449600 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 936) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449600 none CC[C@@H](C)[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 16, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 20, 20, 20, 20, 20, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 937) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449600 none CC[C@@H](C)[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 7, 15, 14, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 17, 17, 17, 17, 17, 15, 15, 15, 2, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449600 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449600 Building ZINC000179449613 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449613 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/938 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449613 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 7, 15, 15, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 7, 13, 13, 13, 16, 16, 16, 16, 16, 15, 15, 15, 2, 6, 14, 14, 14, 14, 14, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/939 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/939' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449613 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 7, 17, 17, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 18, 18, 18, 18, 18, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449613 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 Building ZINC000179449613 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449613 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 938) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449613 none CC[C@@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 7, 15, 15, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 14, 6, 7, 13, 13, 13, 16, 16, 16, 16, 16, 15, 15, 15, 2, 6, 14, 14, 14, 14, 14, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 939) grep: /scratch/xiaobo/365617/xds-8058088.97/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@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449613 none CC[C@@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 16, 7, 17, 17, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 18, 18, 18, 18, 18, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449613 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449613 Building ZINC000179449620 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449620 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/940 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449620 none CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 7, 15, 14, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 17, 17, 17, 17, 17, 15, 15, 15, 2, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/941 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/941' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449620 none CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 16, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 20, 20, 20, 20, 20, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449620 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 Building ZINC000179449620 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179449620 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 940) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179449620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449620 none CC[C@H](C)[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 15, 7, 15, 14, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 13, 13, 13, 17, 17, 17, 17, 17, 15, 15, 15, 2, 6, 15, 15, 15, 15, 15, 6, 13, 13, 13] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 941) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000179449620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179449620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000179449620 none CC[C@H](C)[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 16, 2, 7, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 15, 6, 7, 14, 14, 14, 20, 20, 20, 20, 20, 17, 17, 17, 2, 6, 15, 15, 15, 15, 15, 6, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179449620 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179449620 Building ZINC000179480629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179480629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/942 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/942' -> `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)Nc1ccc2nncn2c1) `ZINC000179480629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179480629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000179480629 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34] 40 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/943 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/943' -> `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)Nc1ccc2nncn2c1) `ZINC000179480629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179480629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000179480629 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179480629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 Building ZINC000179480629 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179480629 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 942) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1) `ZINC000179480629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179480629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000179480629 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 8, 8, 8, 34, 34, 34, 34, 34, 34, 34, 34, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 34, 34, 34, 34] 40 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 943) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1) `ZINC000179480629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179480629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000179480629 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2nncn2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 8, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 38, 38, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 59 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179480629 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179480629 Building ZINC000179496556 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179496556 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/944 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1) `ZINC000179496556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179496556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179496556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 10, 14, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/945 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1) `ZINC000179496556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179496556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179496556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 2, 10, 13, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179496556 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 Building ZINC000179496556 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179496556 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 944) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1) `ZINC000179496556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179496556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179496556 none CCn1cc([C@@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 5, 5, 5, 1, 1, 1, 2, 10, 14, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 16, 16, 16, 16, 16, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 945) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1) `ZINC000179496556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179496556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000179496556 none CCn1cc([C@]([O-])([SiH3])C(=O)N2CCOCC23CCC3)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 6, 6, 6, 1, 1, 1, 2, 10, 13, 14, 14, 14, 14, 14, 14, 14, 14, 6, 6, 17, 17, 17, 17, 17, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6] 50 rigid atoms, others: [4, 5, 6] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179496556 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179496556 Building ZINC000179595797 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179595797 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/946 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n(C)n1) `ZINC000179595797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179595797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000179595797 none CCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 27, 11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 40, 40, 40, 40, 40, 27, 27, 11, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/947 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/947' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n(C)n1) `ZINC000179595797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179595797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000179595797 none CCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 27, 10, 10, 10, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 40, 40, 40, 40, 40, 27, 27, 10, 6, 6, 6, 6, 6, 6, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179595797 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 Building ZINC000179595797 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000179595797 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 946) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n(C)n1) `ZINC000179595797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000179595797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000179595797 none CCCc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 27, 11, 11, 11, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 11, 11, 11, 40, 40, 40, 40, 40, 27, 27, 11, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 947) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n(C)n1) `ZINC000179595797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000179595797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 40 natoms 39 natoms 38 natoms 37 names: ZINC000179595797 none CCCc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 27, 10, 10, 10, 6, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 10, 10, 10, 40, 40, 40, 40, 40, 27, 27, 10, 6, 6, 6, 6, 6, 6, 10, 10, 10] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000179595797 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000179595797 Building ZINC000181358398 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181358398 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/948 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1) `ZINC000181358398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181358398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181358398 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14] 41 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 37 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/949 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/949' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1) `ZINC000181358398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181358398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181358398 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12] 39 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 33 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000181358398 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 Building ZINC000181358398 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000181358398 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 948) grep: /scratch/xiaobo/365617/xds-8058088.97/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]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1) `ZINC000181358398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000181358398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181358398 none C[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14] 41 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 37 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 949) grep: /scratch/xiaobo/365617/xds-8058088.97/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]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1) `ZINC000181358398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000181358398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000181358398 none C[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2cnn(C)c2)C[C@H](C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 5, 5, 7, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 11, 12, 12, 12, 12, 12] 39 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 33 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000181358398 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000181358398 Building ZINC000182429727 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182429727 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/950 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000182429727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182429727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182429727 none CC(C)(CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 11, 11, 11, 11, 11, 11, 19, 19, 57, 4, 10, 12, 12, 10, 12, 12, 10] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/951 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/951' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000182429727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182429727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182429727 none CC(C)(CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 11, 11, 11, 11, 11, 11, 19, 19, 57, 4, 10, 12, 12, 12, 12, 12, 10] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182429727 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 Building ZINC000182429727 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182429727 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 950) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000182429727.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182429727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182429727 none CC(C)(CO)NC(=O)[C@@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 11, 11, 11, 11, 11, 11, 19, 19, 57, 4, 10, 12, 12, 10, 12, 12, 10] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 167 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 951) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CC(C)(CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1) `ZINC000182429727.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182429727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000182429727 none CC(C)(CO)NC(=O)[C@]([O-])([SiH3])c1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 8, 1, 11, 5, 12, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 19, 4, 1, 4, 1, 1, 1, 10, 10, 10, 10, 12, 12, 10, 12, 12, 10, 11, 11, 11, 11, 11, 11, 19, 19, 57, 4, 10, 12, 12, 12, 12, 12, 10] 150 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182429727 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182429727 Building ZINC000182407754 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182407754 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/952 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182407754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407754 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 9, 6, 14, 14, 6, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 4, 9, 9, 9, 9, 9, 14, 14, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/953 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/953' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182407754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407754 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [23, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 10, 7, 18, 18, 7, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 4, 10, 10, 10, 10, 10, 18, 18, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182407754 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 Building ZINC000182407754 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182407754 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 952) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182407754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407754 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 9, 6, 14, 14, 6, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 4, 9, 9, 9, 9, 9, 14, 14, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 953) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182407754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407754 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [23, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 10, 7, 18, 18, 7, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 4, 10, 10, 10, 10, 10, 18, 18, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000182407754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182407754 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407754 Building ZINC000182407774 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182407774 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/954 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182407774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407774 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [23, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 10, 7, 18, 18, 7, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 4, 10, 10, 10, 10, 10, 18, 18, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/955 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/955' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182407774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407774 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 9, 6, 14, 14, 6, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 4, 9, 9, 9, 9, 9, 14, 14, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182407774 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 Building ZINC000182407774 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182407774 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 954) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182407774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407774 none CCn1cc([C@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [23, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 7, 10, 7, 18, 18, 7, 13, 13, 7, 7, 23, 23, 23, 23, 23, 7, 4, 10, 10, 10, 10, 10, 18, 18, 13, 13, 13, 13, 13, 13, 13, 7] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 955) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1) `ZINC000182407774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182407774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000182407774 none CCn1cc([C@@]([O-])([SiH3])C(=O)N[C@](CC)(C(N)=O)C(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 8, 11, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 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: [16, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 9, 6, 14, 14, 6, 11, 11, 6, 6, 16, 16, 16, 16, 16, 6, 4, 9, 9, 9, 9, 9, 14, 14, 11, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182407774 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182407774 Building ZINC000182569973 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182569973 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/956 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000182569973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182569973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182569973 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 18, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 30, 30, 18, 18, 18, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/957 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/957' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000182569973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182569973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182569973 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 15, 29, 29, 15, 15, 15, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182569973 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 Building ZINC000182569973 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182569973 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 956) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000182569973.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182569973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182569973 none C[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 6, 18, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 18, 30, 30, 18, 18, 18, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 957) grep: /scratch/xiaobo/365617/xds-8058088.97/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: C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O) `ZINC000182569973.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182569973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182569973 none C[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc2c(c1)CCC2)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 8, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 5, 15, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 15, 29, 29, 15, 15, 15, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 29, 29] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 103 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182569973 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182569973 Building ZINC000182587892 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182587892 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/958 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1) `ZINC000182587892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182587892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587892 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 8, 17, 17, 8, 17, 17, 9, 9, 9, 9, 9, 9, 4, 27, 27, 81, 17, 17, 8, 17, 17, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 240 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/959 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/959' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1) `ZINC000182587892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182587892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587892 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 8, 16, 16, 15, 16, 16, 9, 9, 9, 9, 9, 9, 4, 22, 22, 66, 16, 16, 16, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182587892 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 Building ZINC000182587892 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182587892 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 958) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1) `ZINC000182587892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182587892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587892 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 8, 17, 17, 8, 17, 17, 9, 9, 9, 9, 9, 9, 4, 27, 27, 81, 17, 17, 8, 17, 17, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 240 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 959) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1) `ZINC000182587892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182587892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587892 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 22, 8, 16, 16, 15, 16, 16, 9, 9, 9, 9, 9, 9, 4, 22, 22, 66, 16, 16, 16, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182587892 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587892 Building ZINC000182587914 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182587914 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/960 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1) `ZINC000182587914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182587914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587914 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 23, 8, 16, 16, 8, 16, 16, 9, 9, 9, 9, 9, 9, 4, 23, 23, 69, 16, 16, 8, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/961 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/961' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1) `ZINC000182587914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182587914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587914 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 8, 17, 17, 8, 17, 17, 8, 8, 8, 8, 8, 8, 4, 27, 27, 81, 17, 17, 8, 17, 17, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182587914 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 Building ZINC000182587914 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000182587914 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 960) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1) `ZINC000182587914.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000182587914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587914 none Cn1cc([C@@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [9, 9, 9, 1, 1, 1, 1, 4, 4, 4, 8, 8, 23, 8, 16, 16, 8, 16, 16, 9, 9, 9, 9, 9, 9, 4, 23, 23, 69, 16, 16, 8, 16, 16, 9] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 208 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 961) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1) `ZINC000182587914.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000182587914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000182587914 none Cn1cc([C@]([O-])([SiH3])C(=O)N[C@H](CO)c2ccccc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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: [8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 8, 8, 27, 8, 17, 17, 8, 17, 17, 8, 8, 8, 8, 8, 8, 4, 27, 27, 81, 17, 17, 8, 17, 17, 8] 150 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 239 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000182587914 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000182587914 Building ZINC000183549908 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183549908 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/962 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCCNC(C)=O) `ZINC000183549908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183549908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000183549908 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCCNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 22, 43, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 40, 41, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/963 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/963' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCCNC(C)=O) `ZINC000183549908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183549908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000183549908 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCCNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 23, 44, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 26, 26, 42, 41, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183549908 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 Building ZINC000183549908 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183549908 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 962) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCCNC(C)=O) `ZINC000183549908.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183549908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000183549908 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCCNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 22, 43, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 25, 25, 40, 41, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 230 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 963) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCCNC(C)=O) `ZINC000183549908.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183549908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC000183549908 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCCNC(C)=O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 3, 3, 3, 15, 23, 44, 49, 49, 49, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 26, 26, 42, 41, 49, 49, 49, 49] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 237 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183549908 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183549908 Building ZINC000183722972 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183722972 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/964 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1) `ZINC000183722972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183722972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000183722972 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 27, 27, 12, 12, 12, 9, 9, 9, 9, 10, 27, 27, 27] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/965 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/965' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1) `ZINC000183722972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183722972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000183722972 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 27, 27, 12, 12, 12, 9, 9, 9, 9, 10, 27, 27, 27] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183722972 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 Building ZINC000183722972 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183722972 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 964) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1) `ZINC000183722972.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183722972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000183722972 none COc1ccccc1[C@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 27, 27, 12, 12, 12, 9, 9, 9, 9, 10, 27, 27, 27] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 965) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1) `ZINC000183722972.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183722972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC000183722972 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)Nc1n[nH]c(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 8, 6, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [12, 9, 9, 9, 1, 9, 9, 1, 1, 1, 1, 10, 10, 10, 27, 27, 27, 27, 27, 27, 12, 12, 12, 9, 9, 9, 9, 10, 27, 27, 27] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183722972 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183722972 Building ZINC000183745220 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745220 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/966 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncc[nH]1) `ZINC000183745220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183745220 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncc[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.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 27, 33, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 33, 33, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/967 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/967' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncc[nH]1) `ZINC000183745220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183745220 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncc[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.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 7, 7, 7, 26, 34, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 7, 26, 26, 34, 34, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183745220 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 Building ZINC000183745220 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183745220 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 966) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncc[nH]1) `ZINC000183745220.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183745220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183745220 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCc1ncc[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.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 27, 33, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 33, 33, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 162 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 967) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncc[nH]1) `ZINC000183745220.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183745220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183745220 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCc1ncc[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.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 1, 8, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 2, 5, 5, 1, 1, 1, 1, 7, 7, 7, 26, 34, 38, 38, 38, 38, 38, 5, 5, 5, 5, 5, 5, 5, 7, 26, 26, 34, 34, 38, 38] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 157 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183745220 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183745220 Building ZINC000183579832 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183579832 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/968 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000183579832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183579832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183579832 none CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [45, 38, 19, 19, 10, 19, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 39, 39, 19, 10, 10, 7, 7, 3, 3, 3, 3, 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/969 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/969' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000183579832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183579832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183579832 none CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [45, 38, 19, 19, 10, 19, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 39, 39, 19, 10, 10, 7, 7, 3, 3, 3, 3, 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183579832 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 Building ZINC000183579832 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183579832 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 968) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000183579832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183579832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183579832 none CCCNC(=O)CCNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [45, 38, 19, 19, 10, 19, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 39, 39, 19, 10, 10, 7, 7, 3, 3, 3, 3, 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 969) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000183579832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183579832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 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: ZINC000183579832 none CCCNC(=O)CCNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 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: [45, 38, 19, 19, 10, 19, 7, 3, 3, 1, 3, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 48, 48, 48, 48, 48, 39, 39, 19, 10, 10, 7, 7, 3, 3, 3, 3, 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: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183579832 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183579832 Building ZINC000183581933 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183581933 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/970 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnn(C)c1) `ZINC000183581933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183581933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183581933 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 20, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/971 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/971' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnn(C)c1) `ZINC000183581933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183581933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183581933 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 20, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183581933 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 Building ZINC000183581933 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183581933 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 970) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnn(C)c1) `ZINC000183581933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183581933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183581933 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 20, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 971) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnn(C)c1) `ZINC000183581933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183581933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183581933 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 20, 45, 45, 45, 45, 45, 3, 3, 3, 3, 3, 3, 3, 4, 20, 20, 45, 45, 45, 45, 45] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183581933 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183581933 Building ZINC000183594403 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183594403 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/972 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1cccn1) `ZINC000183594403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183594403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183594403 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 29, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 29, 29, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/973 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/973' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1cccn1) `ZINC000183594403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183594403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183594403 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 30, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 30, 30, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183594403 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 Building ZINC000183594403 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183594403 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 972) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1cccn1) `ZINC000183594403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183594403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183594403 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 21, 29, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 5, 21, 21, 29, 29, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 973) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1cccn1) `ZINC000183594403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183594403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183594403 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 1, 8, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 6, 6, 6, 22, 30, 41, 41, 41, 41, 3, 3, 3, 3, 3, 3, 3, 6, 22, 22, 30, 30, 41, 41, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183594403 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183594403 Building ZINC000183970167 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183970167 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/974 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1) `ZINC000183970167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183970167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970167 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/975 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/975' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1) `ZINC000183970167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183970167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970167 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 10, 10, 10, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183970167 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 Building ZINC000183970167 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183970167 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 974) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1) `ZINC000183970167.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183970167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970167 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 44, 44, 44, 44, 44, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 44] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 975) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1) `ZINC000183970167.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183970167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970167 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 10, 10, 10, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183970167 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970167 Building ZINC000183970187 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183970187 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/976 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1) `ZINC000183970187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183970187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970187 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 10, 10, 10, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/977 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/977' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1) `ZINC000183970187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183970187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970187 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183970187 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 Building ZINC000183970187 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183970187 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 976) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1) `ZINC000183970187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183970187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970187 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 6, 10, 10, 10, 43, 43, 43, 43, 43, 4, 4, 4, 4, 4, 4, 4, 6, 10, 10, 10, 43] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 977) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1) `ZINC000183970187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183970187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000183970187 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1nc[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 8, 1, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 2, 6, 6, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 41, 41, 41, 41, 41, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 41] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183970187 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183970187 Building ZINC000183947131 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183947131 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/978 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1) `ZINC000183947131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183947131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000183947131 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 40, 40, 24, 9, 9, 9, 7, 7, 7, 7, 6, 24, 24, 24, 40, 40, 40, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/979 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/979' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1) `ZINC000183947131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183947131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000183947131 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 40, 40, 24, 9, 9, 9, 7, 7, 7, 7, 6, 24, 24, 24, 40, 40, 40, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183947131 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 Building ZINC000183947131 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183947131 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 978) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1) `ZINC000183947131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183947131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000183947131 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 40, 40, 24, 9, 9, 9, 7, 7, 7, 7, 6, 24, 24, 24, 40, 40, 40, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 979) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1) `ZINC000183947131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183947131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC000183947131 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NC1CN(C(C)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 2, 7, 7, 1, 1, 1, 1, 6, 6, 6, 24, 24, 24, 40, 40, 24, 9, 9, 9, 7, 7, 7, 7, 6, 24, 24, 24, 40, 40, 40, 24, 24] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183947131 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183947131 Building ZINC000183951065 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183951065 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/980 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000183951065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183951065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183951065 none CN(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 23, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 8, 23, 23, 23, 23, 23, 23, 8, 8, 8, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/981 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/981' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000183951065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183951065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183951065 none CN(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 7, 24, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183951065 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 Building ZINC000183951065 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000183951065 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 980) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000183951065.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000183951065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183951065 none CN(C)c1cccc(NC(=O)[C@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 8, 23, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 8, 23, 23, 23, 23, 23, 23, 8, 8, 8, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 981) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CN(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1) `ZINC000183951065.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000183951065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000183951065 none CN(C)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'N.ar', '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, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 7, 24, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 12, 12, 12, 12, 12, 7, 24, 24, 24, 24, 24, 24, 7, 7, 7, 4, 12, 12, 12, 12, 12] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000183951065 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000183951065 Building ZINC000184257754 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184257754 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/982 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184257754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257754 none CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 6, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 8, 8, 8, 8, 8, 4, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/983 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/983' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184257754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257754 none CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 5, 6, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 5, 10, 10, 10, 10, 10, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000184257754 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 Building ZINC000184257754 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184257754 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 982) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184257754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257754 none CCCC[C@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 6, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 8, 8, 8, 8, 8, 4, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 983) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184257754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257754 none CCCC[C@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 5, 6, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 5, 10, 10, 10, 10, 10, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000184257754 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257754 Building ZINC000184257772 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184257772 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/984 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184257772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257772 none CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 5, 6, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 5, 10, 10, 10, 10, 10, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/985 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/985' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184257772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257772 none CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 6, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 8, 8, 8, 8, 8, 4, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000184257772 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 Building ZINC000184257772 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000184257772 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 984) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000184257772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257772 none CCCC[C@@H](NC(=O)[C@@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 10, 5, 6, 15, 15, 15, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 5, 10, 10, 10, 10, 10, 5, 15, 15, 15] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 985) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC) `ZINC000184257772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000184257772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC000184257772 none CCCC[C@@H](NC(=O)[C@]([O-])([SiH3])c1cnn(CC)c1)C(=O)OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', '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, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 1, 1, 11, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 14, 12, 6, 2, 6, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 8, 4, 6, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 4, 8, 8, 8, 8, 8, 4, 13, 13, 13] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000184257772 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000184257772 Building ZINC000185480385 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185480385 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/986 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1) `ZINC000185480385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185480385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185480385 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 21, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 21, 21, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/987 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/987' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1) `ZINC000185480385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185480385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185480385 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 21, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 21, 21, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185480385 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 Building ZINC000185480385 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185480385 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 986) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1) `ZINC000185480385.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185480385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185480385 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 21, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 21, 21, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 987) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1) `ZINC000185480385.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185480385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185480385 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 5, 5, 5, 16, 21, 40, 40, 40, 40, 3, 3, 3, 3, 3, 3, 3, 5, 16, 16, 21, 21, 40, 40, 40] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185480385 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185480385 Building ZINC000185490912 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185490912 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/988 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000185490912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185490912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185490912 none CCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 18, 28, 6, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 43, 43, 43, 43, 43, 28, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/989 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/989' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000185490912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185490912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185490912 none CCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 18, 28, 6, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 43, 43, 43, 43, 43, 28, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185490912 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 Building ZINC000185490912 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185490912 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 988) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC) `ZINC000185490912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185490912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185490912 none CCNC(=O)CNC(=O)[C@@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 18, 28, 6, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 43, 43, 43, 43, 43, 28, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 989) grep: /scratch/xiaobo/365617/xds-8058088.97/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: CCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC) `ZINC000185490912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185490912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000185490912 none CCNC(=O)CNC(=O)[C@]([O-])([SiH3])c1ccccc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [43, 28, 28, 18, 28, 6, 6, 1, 6, 1, 1, 1, 3, 3, 2, 3, 3, 3, 3, 43, 43, 43, 43, 43, 28, 18, 18, 6, 3, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 186 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185490912 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185490912 Building ZINC000185496430 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185496430 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/990 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C) `ZINC000185496430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185496430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185496430 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 25, 47, 46, 46, 47, 47, 47, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/991 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/991' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C) `ZINC000185496430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185496430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185496430 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 25, 47, 47, 47, 47, 47, 47, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185496430 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 Building ZINC000185496430 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000185496430 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 990) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C) `ZINC000185496430.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185496430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185496430 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 25, 47, 46, 46, 47, 47, 47, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 991) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C) `ZINC000185496430.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000185496430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC000185496430 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)NC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 1, 11, 8, 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, 9, 8, 10, 11, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 3, 5, 5, 1, 1, 1, 1, 5, 5, 5, 25, 47, 47, 47, 47, 47, 47, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185496430 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185496430 Building ZINC000888109500 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888109500 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/992 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109500 none COC(=O)[C@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 15, 15, 15, 15, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/993 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/993' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109500 none COC(=O)[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888109500 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 Building ZINC000888109500 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888109500 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 992) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109500 none COC(=O)[C@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 15, 15, 15, 15, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 993) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888109500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109500 none COC(=O)[C@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 22, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 6, 6, 2, 6, 6, 6, 22, 22, 22, 9, 9, 9, 9, 6, 6, 2, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888109500 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109500 Building ZINC000888109504 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888109504 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/994 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888109504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109504 none COC(=O)[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 23, 23, 23, 12, 12, 12, 12, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/995 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/995' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888109504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109504 none COC(=O)[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 15, 15, 15, 15, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888109504 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 Building ZINC000888109504 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000888109504 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 994) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000888109504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109504 none COC(=O)[C@@H]1CCN1C(=O)[C@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 12, 23, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 23, 23, 23, 12, 12, 12, 12, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 995) grep: /scratch/xiaobo/365617/xds-8058088.97/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: COC(=O)[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1) `ZINC000888109504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000888109504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 37 natoms 36 natoms 35 natoms 34 names: ZINC000888109504 none COC(=O)[C@@H]1CCN1C(=O)[C@@]([O-])([SiH3])c1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 26, 15, 15, 15, 15, 7, 1, 7, 1, 1, 1, 6, 6, 1, 6, 6, 6, 26, 26, 26, 15, 15, 15, 15, 6, 6, 1, 6, 6, 6, 6] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000888109504 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000888109504 Building ZINC000648451651 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648451651 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/996 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1) `ZINC000648451651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648451651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451651 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 4, 4, 1, 1, 1, 1, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 54, 4, 4] 66 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/997 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/997' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1) `ZINC000648451651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648451651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451651 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 23, 23, 23, 27, 27, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 81, 5, 5] 90 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 167 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000648451651 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 Building ZINC000648451651 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648451651 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 996) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1) `ZINC000648451651.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648451651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451651 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [3, 2, 4, 4, 1, 1, 1, 1, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 54, 4, 4] 66 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 997) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1) `ZINC000648451651.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648451651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451651 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 5, 5, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 23, 23, 23, 27, 27, 5, 5, 5, 5, 5, 5, 5, 23, 23, 23, 23, 23, 23, 81, 5, 5] 90 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 167 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000648451651 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451651 Building ZINC000648451653 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648451653 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/998 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1) `ZINC000648451653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648451653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451653 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 4, 4, 1, 1, 1, 1, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 60, 4, 4] 69 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/999 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/999' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1) `ZINC000648451653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648451653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451653 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 6, 6, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 23, 23, 23, 27, 27, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 81, 6, 6] 90 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000648451653 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 Building ZINC000648451653 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648451653 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 998) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1) `ZINC000648451653.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648451653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451653 none Cc1ccc([C@@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 4, 4, 1, 1, 1, 1, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 60, 4, 4] 69 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 119 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 mkdir: created directory `1' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 1 (index: 999) grep: /scratch/xiaobo/365617/xds-8058088.97/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: Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1) `ZINC000648451653.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648451653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC000648451653 none Cc1ccc([C@]([O-])([SiH3])C(=O)N2CCOC[C@H]2C(=O)O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 12, 5, 5, 7, 1, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 3, 7, 7, 7, 7, 5, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 6, 6, 1, 1, 1, 1, 13, 13, 23, 23, 23, 23, 23, 23, 23, 27, 27, 6, 6, 6, 6, 6, 6, 6, 23, 23, 23, 23, 23, 23, 81, 6, 6] 90 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 171 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000648451653 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/0.* 1: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653/1.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000648451653 Building ZINC000185516062 mkdir: created directory `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000185516062 mkdir: created directory `0' /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062/0 /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/365617/xds-8058088.97/working/3D/1000 `/scratch/xiaobo/365617/xds-8058088.97/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1) `ZINC000185516062.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000185516062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC000185516062 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCC(=O)N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.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, 11, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 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: [3, 3, 3, 3, 2, 3, 3, 1, 1, 1, 1, 4, 4, 4, 18, 45, 45, 48, 48, 48, 48, 3, 3, 3, 3, 3, 3, 3, 4, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062 /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Finished preparing ZINC000185516062 Recording results /scratch/xiaobo/365617/xds-8058088.97/working /scratch/xiaobo/365617/xds-8058088.97 Appending to /scratch/xiaobo/365617/xds-8058088.97/finished/xds.* 0: /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062/0.* Removing working files in /scratch/xiaobo/365617/xds-8058088.97/working/building/ZINC000185516062 /scratch/xiaobo/365617/xds-8058088.97 Compressing combined databse files /scratch/xiaobo/365617/xds-8058088.97/finished/xds.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/365617/xds-8058088.97/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/365617/xds-8058088.97/working/3D/1001' removed directory: `/scratch/xiaobo/365617/xds-8058088.97/working/3D' rmdir: removing directory, `/scratch/xiaobo/365617/xds-8058088.97/working/building' rmdir: removing directory, `/scratch/xiaobo/365617/xds-8058088.97/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/365617/xds-8058088.97' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xds' `/scratch/xiaobo/365617/xds-8058088.97/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xds/finished' `/scratch/xiaobo/365617/xds-8058088.97/finished/xds.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xds/finished/xds.db2.gz' removed `/scratch/xiaobo/365617/xds-8058088.97/finished/xds.db2.gz' removed directory: `/scratch/xiaobo/365617/xds-8058088.97/finished' removed directory: `/scratch/xiaobo/365617/xds-8058088.97'